This happens so often in the Lupin III movies that it becomes a shock when Lupin doesn't have to fork over the treasure-of-the-film.
Pokémon episode "Mantine Overboard". Team Rocket letting Ash and his friends do the hard work of finding a treasure chest in a sunken ship, then stepping in and taking it away from them.
In Kamikaze Kaitou Jeanne, in both the anime and the manga version, the titular character spends a good part of the story unknowingly working for the devil.
Averted in Chouja Reideen, where the heroes are completely unaware of the MacGuffins' existence until late in the series.
In Transformers: Kiss Players, the Sparkbots call upon Marissa Faireborn, Shaoshao Li, and Atari Hitotonari to travel the multiverse and gather fragments of the Allspark. When they succeed, the Sparkbots reveal that the fragments were actually Angolmois, Unicron's lifeforce. They thank the girls for doing their dirty work for them and revive Unicron. Fortunately, Primus appears and defeats the Dark God.
In the Legacy story arc in the Batman comics, Ra's al Ghul used Catwoman this way to get to an ancient wheel that was a recipe for plagues.
The Riddler also tried it on Catwoman during the "When In Rome" storyline, using her to get a ring that makes the wearer the head of the Mafia. He ends up with a fake ring and a lungful of Scarecrow's fear gas, giving him visions of everyone around him on the plane as the Joker.
In Captain America Annual #13, the Red Skull is after Hitler's Strongbox. The Skull learns the strongbox is located in the castle of Albert Malik, the Communist who impersonated the Skull in the 1950s. The Skull, knowing that Captain America will not resist attempting to stop him, issues a challenge which contains the strongbox's location. Cap makes his way through Malik's booby-trapped dungeon to the vault. At which point the Skull comes up behind Cap, death ray in hand, and tells him "I must thank you for activating all the many defenses Malik devised to protect the true strongbox." When an angry Cap declares "So you didn't arrive here first! You maneuvered me into being your stalking horse!" the Skull responds "You should feel flattered. I had so much faith in you surviving Malik's death traps, I followed hard on your heels."
In With Strings Attached, the four knock themselves out collecting the three pieces of the Vasyn, one by one. Returning triumphantly with the (much smaller) third piece, they are horrified to discover the other two (huge) pieces missing! (Paul: Who would want them? Who could steal them? John: We could!) Subverted in that the four had no idea anyone else would want the Vasyn, and the thieves didn't even know the four were fetching it until they returned to Ta'akan and found the first two pieces sitting there.
In Queen Of All Oni, the only method Jade has for tracking the masks on her own is astral projection, which she doesn't trust because she can't control it. So, she has bugs planted in Uncle's shop, so that whenever Jackie and the others discover the location of a mask, she can simply follow them there. This is also what led her to the first tablet of the Teachings of Eternal Shadow, which set off the story's secondary Plot Coupon hunt.
The Tears Of Gaia: When Maugoth learns of the Tears, he decides to let the Mane Six do all the hard work of finding them, so that he and his fellow Blightlings don't have to worry about any of the potential threats protecting them.
In the film Oceans Thirteen, Linus Caldwell and his father are about to escape Banks' building with some obscenely valuable diamonds when they are confronted by Francois Toulour (the antagonist of the previous films), who takes the diamonds at gunpoint. Subverted, however, after Toulour leaves the protagonists reveal that the diamonds they gave to Toulour were fakes, and they escape with the real ones.
In The Fifth Element, Leeloo fights off a squad of Mangalores to retrieve a case of Applied Phlebotinum stones, only for Zorg to take it from her at gunpoint. Subverted when the case turns out to be empty.
In For Your Eyes Only, James Bond and Melina salvage the ATAC after being attacked by some of Kristato's mooks, only to surface and find Kristatos and his other mooks, having killed their crew.
In Bullet to Beijing, Harry Palmer is told by his contact Louis that one component of a deadly biological weapon will be on the bullet train to Beijing. When the train is nearly at its destination, Harry discovers that the vial is in the doll that Louis's grandson gave him before he began.
Both National Treasure movies involve the Big Bad luring Benjamin Gates into some treasure hunt filled with riddles, letting him do the hard work in solving them and leading the villain to the treasure. Gates is all too willing.
Percy Jackson And The Olympians The Lightning Thief invokes this. Percy was used to carry the master bolt to Hades by Luke. After that, he delivers it to Zeus. Of course, some of the gods thought Percy was the original thief from the start, for no adequately explained reason.
In Harry Potter and the Philosopher's Stone: Dumbledore hides the Philosopher's Stone within the Mirror of Erised, with the condition that it will only give the stone to someone who wants to find it but not use it for themselves. When Quirrel demands Harry look in the mirror and see where the stone is, it's transported to his pocket - unfortunately for Quirrel, he can't so much as touch Harry without The Power of Love burning him.
In Order of the Phoenix, Harry breaks into the Ministry of Magic based on visions (from Voldemort) which everyone he tells about urge him to block in order to get the prophecy for Voldemort. Only the people the prophecy refers to can take it, and Voldemort doesn't want the Ministry to stop conveniently denying his return. It's two tropes in one; a pretty case of a Batman Gambit by Voldemort that results in Harry almost serving as a MacGuffin Delivery Service
The plot of the Deptford Mice prequel Thomas is basically one huge example of this trope. The difference being, the chessmasters behind the good guys actually intend the bad guys to get hold of the MacGuffin, because they've left it hallowed and thus useless for resurrecting the monster.
In Dead Beat of The Dresden Files, the villains are all looking for both the Word of Kemmler, and a book to summon The Erlking. Harry is the first to find both, and ends up summoning the Erlking himself to keep the villains from using him...at which point said villains show up, club him over the head, and take both. Notably, Harry at least has the foresight to speed read and memorize the Word of Kemmler as soon as he gets it just in case.
In The Lightning Thief Percy is used by Luke and Ares in an attempt to deliver Zeus's master lightning bolt to Kronos. He then needs to deliver it to Zeus to prevent a war of the gods.
Live Action TV
Doctor Who: The Key to TimeStory Archangs a lampshade on this, with the heroes expecting the Big Bad to try to get every part of the Key. Eventually they discover that he simply got his Dragon to look after the last part and wait for the others to come along, in order to save himself the trouble. "The Five Doctors" has a villainous Time Lord get the Doctor's five incarnations (and various of his companions) to retrieve the secret of (true) immortality for him.
Also found in some of the Animated Specials.
The Librarian: Quest for the Spear. If the Sword of Destiny hasn't been found in all these years, why don't they assume it's safe where it is?
Subverted on Blake's 7: The crew of a prison ship find an abandoned space ship in the middle of nowhere and decide to have a few of the convicts go on first to find booby traps. The convicts are the heroes and they take the ship as their own.
In Tin Man, Azkadelia has spent years unsuccessfully searching for the Emerald of the Eclipse, which she needs to bring her plan to plunge the O.Z. into eternal darkness to fruition. Enter DG and friends, who decide that they have to find the Emerald to stop her. Not one of them suggests that they can foil Azkadelia's plot by just sitting down and twiddling their thumbs until the eclipse has passed.
Once Upon a Time in Wonderland: In order to complete his spell to rewrite the laws of magic, Jafar discovers that he needs to restore the Knave of Hearts' missing heart. After Alice and Cyrus travel to Storybrooke to retrieve it to stop him getting it he simply takes it from them. However, in the battle they are able to take his staff, which is another necessary component of the spell.
Dungeons & Dragons adventure "The Apocalypse Stone". The first half or so consists of the PC's going on a false mission on behalf of the Big Bad to get him the magical Stone he covets but is under a Magically-Binding Contract not to remove. Unfortunately for everyone (well, except maybe members of the Doomguard), it's not just a MacGuffin; the Stone was actually holding the world together, and removing it from its place has some nasty effects.
Journal of the Travellers' Aid Society #23 Amber Zone "The Birthday Plot". Inkula, a Grand Master of the Irklan religious sect, plans to let the PCs find the evidence of his crimes for him, kill them and take the evidence.
The MegaTraveller Journal #3, adventure "Rapid Repo". The PCs are ordered to obtain the vital components of a prototype deep radar system on the Vargr-occupied planet Depot. The head of the Vargr counter-intelligence knows about the deep radar but not exactly where it is. When he learns that the PCs are coming he decides to let them find the deep radar and then take it from them.
In the original Tomb Raider, Lara inadvertently helps Natla reclaim her original Scion piece, and also the other two.
Same in Tomb Raider 2, Tomb Raider 3, Tomb Raider Revelatio- Okay, this happens a lot. Pretty much the basic plot of every game is Lara beating the villain to the treasure of the game, then somehow losing it to the baddie anyway and having to tackle a supernatural final boss.
Zig-zagged in the case of Tomb Raider 3, in that Lara collects the final four artifacts in the game for her employer, Dr. Willard. While his claimed intentions were that of merely archaeological curiosity, it turns out that he was using Lara to collect the artifacts to power up an ancient laboratory of "accelerated evolution". Having seen the results of previous experiments, resulting in grotesque and vicious mutations of the human guinea pigs, Lara turns rogue and later kills Dr. Willard, getting the artifacts back.
Erazor Djinn too in Sonic and the Secret Rings. And he almost killed Sonic, too!
Final Fantasy IV sometimes does this with elemental crystals. Notably when after the final dark crystal in the sealed cave, and after fighting the incredibly annoying evil wall, Kain reaffirms his status of hypnosis and makes off with the crystal, bringing it back to Golbez. Keep in mind that the Sealed Cave is riddled with instant death dealing Trapdoors, powerful monsters, and That One Boss, so maybe Golbez and Zemus, who's controlling him had it in his best interest to let Cecil do the dirty work for him rather than pour in minions or do it himself.
Hell, it's outright stated that Golbez can't get into the cave. You even leave him to try for the duration for an entire subquest, and Golbez still fails to get into the cave, because you need a special key to get in at all. You'd think after all that, Cecil and the gang would realize that the crystal was perfectly safe right where it was, but nooooOOOOoooo.
To be fair, Golbez and the Baron military have already successfully taken several "impossible to steal" crystals, including the one that the Dwarf King was almost literally sitting on. It's not exactly a bad assumption on Cecil's part that the sealed gate won't stop him for long. Given his past records however, the idea that it's safer in his hands might be a stretch.
Giott, the King of the Dwarves implies that given enough time, Golbez could force the deal on the door with raw magical power. The plan was supposed to be moving the crystal to another place before Golbez found out. Clearly, it didn't work.
Not only that, but in the DS remake, going to your inventory screen has whichever character is in front display a little thought balloon with what they, personally, think of the situation. On your way back up through the cave, Kain's reads: "This feeling...I've felt it before..." then, "No...no! Not again!" Mind telling us that out loud there, Kain?
This trope is almost inverted during gameplay, when Cecil and Co. hatch a plan to storm the Big Bad's stronghold to get the crystals that they've obtained over the course of the game. Unfortunately, it turns out that the first step our heroes take into the Crystal Room is onto a trap door - even if everyone has the 'Float' status.
The first major quest in Final Fantasy IV is this trope. Cecil and Kain take a ring to the Village of Mist. Once they get there the ring burns the town to the ground. Although, in this case, the Big Bad certainly could have done it himself.
And Final Fantasy IV: The After Years has you doing the exact same thing, except at least this time it's mentioned that the villains might be able to get through the seal using brute force.
This was used on the NES Ninja Gaiden game: Ryu Hayabusa gained one of the two Demon Statues that would awaken Jashin, only to have to give them up to Jaquio who was holding Irene Lew hostage. He was then promptly dropped down a conveniently non-lethal pit for his trouble.
An interesting version of this trope occurs in the 2007 Ghost Rider game. The player travels to various locales to hunt down Blackheart's demons who threaten to open the gateway to Hell on Earth, only to find that the gate opens anyway, as the path the Rider took drew an evil symbol on the Earth in the flames left behind by the Rider's bike.
The Elder Scrolls III: Morrowind has a rare justified example, as the player brings the Wraithguard, a magical gauntlet required to handle the tools of Kagrenac, to Dagoth Ur's lair in order to destroy the Heart of Lorkhan which is housed there. If the player were to be slain, Dagoth Ur would then have all the tools necessary to tap into the heart once again. Justified, since the tools are needed to destroy the heart and actually kill the Physical God Dagoth Ur.
One of the side quests in The Elder Scrolls IV: Oblivion is based around this trope. (It's even called "Nothing You Can Possess," in reference to the Raiders of the Lost Ark quote.) A wealthy collector hires you to retrieve a particular carving from a ruin. Upon exiting the ruin, you're immediately accosted by a rival treasure hunter and his hired goons, demanding that you turn over the carving.
Something similar happens in the Mages' Guild quest where you must retrieve a replacement amulet since the original was stolen. As soon as you grab it, you are confronted by the butt-ugly Nord whom you knew did it all along.
The Elder Scrolls V: Skyrim has an example in the Dawnguard expansion. When storming Castle Volkihar you bring with you the key pieces of Harkon's plan, Auriel's Bow and Serana. If the Dovahkiin were to be killed, Harkon would presumably enact his plan right then and there.
Also used in a side quest in Knights of the Old Republic, on the planet Korriban. Subverted if you choose to simply kill the student trying to threaten you, or if you give him a fake and let Uthar do your dirty work for you.
This happens to the titular protagonist of Shantae after obtaining the last Elemental Stone. That genie that looks suspiciously like the Big Bad who seemed to know everything about the Stones and would stop at nothing to help you get the last one? You shouldn't have been so surprised when you exited the dungeon only to be tackled and robbed by her.
Metal Gear Solid and its PAL key again. The bad guys were counting on you obtaining the keycard, but in the course of the game you defy the odds to get it back, find out how it works, and use it to activate the nuclear weapon.
Very much true in Fallout 3. Very galling as you know that the big bad is looking for the MacGuffin, and although you should by rights be able to torch him, his two little helpers and half his army (and in fact do exactly that later in the game) you cannot stop him from stealing the G.E.C.K. in a cutscene.
Well, technically you can. In the brief period that you have the G.E.C.K., you can try to activate it. It then warns you that it will destroy everything in a several-mile radius for raw materials. You can then confirm that you want to activate it...
In Terranigma you spend the majority of the game reviving the desolate planet Earth, with the last piece revived being Beruga who wants to wipe out the majority of what you just spent the first 75% of the game reviving and preserve the remainder as technologically-created zombies, according to the plans of Dark Gaia, for whom you've been unwittingly working the whole time. Oh, and did I mention that Beruga was the one responsible for wiping out all life on the surface world in the first place?
In The Force Unleashed, you spend the second act collecting the Rebel leaders and organizing the Rebellion for Vader. He then takes them all, revealing that he never intended to use the Rebellion as a distraction so you could kill the Emperor, but just wanted to round up and destroy all opposition to the Empire.
This then backfires in predictable fashion; the rebellion, having been organized together by the player, is suddenly a credible threat against the Empire rather than a bunch of scattered malcontents.
This happens in Ōkami - partly. Having retreived the Fox Rods from inside the Water Dragon, Amaterasu then proceeds to hand them over to Rao, who then turns out to be Ninetails in disguise.
This is the entire plot of Mortal Kombat Deception's Konquest mode.
In Summoner, you spend the first third of the game gathering up the four Rings of Summoning so that you can turn yourself into an invincible warrior by using the Forge of Urath on your ringed hand. As it turns out, all that does is burn off your hand, release four demigodly demons trapped within the rings, and allow your traitorous girlfriend to sell you off to The Empire. All thanks to your mentor, who was possessed by the most powerful of the demons. Now you need to beg the Khosani for four new rings, and imprison all four demons again. Nice Job Breaking It, Hero.
Happens right off the bat in Golden Sun, where Saturos and Menardi follow Isaac into Sol Sanctum to take the Elemental Stars as soon as you've retrieved them.
Happens yet again at the climax of the second game, when Felix and company reach the top of the final lighthouse only to learn that completing their mission will give Alex the ultimate power of the Golden Sun.
And Dark Dawn takes it to a ridiculous extent. Right from square one, the villains let slip that they're manipulating you. At one point, the Big Bad even gives you a MacGuffin that you need to fulfill your (read: his) ambitions. Quite literally everything you do in the game with the sole exception of winning the final boss fight is exactly what the villains need you to do. And in fact even that, and what you do after beating the final boss, is what Alex wants you to do. The game is a rare instance of 100% of the plot being a MacGuffin Delivery Service.
Oddly enough, shows up in Bomber Man 64. Altair is hyped up for the entire game to be the Big Bad, except if you've gotten all of the Gold Cards. If you do that, instead of fleeing after you've beaten him, Sirius, the guy who has been helping you out, showing up on almost every level and giving you hints, and dropping you the Remote Bomb powerup before every boss, flies in and kills him, then points out that the guys you've been fighting stole the superweapon from him, and you've been unwittingly helping him recover it. After that, all of the hint-givers in the previous levels tell you that you should die because it would be easier. They aren't lying. The hidden final world is WAY harder than anything and everything that came before it.
Bomberman Hero did this as well, after you've finally recovered all of the data disks, you hand them over to what you think is Princess Millian. It turns out to be Natia in disguise.
Not played straight in Gun. The protagonist retrieves something from a safe, but the bad guy who shows up to collect it doesn't bother to actually snatch the item before gloating about the situation. So the protagonist just tosses the thing back in the safe and slams the door.
Eye of the Beholder 3. A mysterious figure sends you off to kill a lich. Once you finally manage, it turns out to have been a good lich (despite the fact that he, you know, tried to kill you) and the mysterious figure teleports in, gets an unnamed MacGuffin, reveals himself to be the evil dark god, and flees. The rest of the game is spent chasing him.
There is a Nancy Drew game where you discover that the Aztec stone pillar is hollow and contains an important artifact. When you open it, the villain immediately appears, takes the artifact, and shuts you inside the pillar (from whence you have to escape). There's no option of, say, just telling people that the pillar opens.
In Crash Bandicoot 2: Cortex Strikes Back, the goal of the game is to gather Crystals for Cortex so he can shield the planet from a planetary alignment (Cortex's actual plans for them, of course, aren't as heroic as Crash's: Instead he wants to use the crystals to power a massive mind control device).
Uka Uka: You seem to have overlooked one small detail, you little orange delivery boy! Now that you have gathered all the Crystals, all we have to do... is TAKE THEM FROM YOU!
And subverted by the fact that Crash wins those battles. It's even more grandiose in the 100% Completion boss fight, where Uka Uka gloats that he'll be able to achieve ultimate power with both the crystals and the gems.
Uka Uka: Yes, it is true! The bandicoot has brought all of the crystals, and all of the gems. Ultimate power is mine! The world as we know it is about to end.
In Final Fantasy XII the empire improvises one of these. It turns out that Vossler, who joins your party on the way to the Tomb of Raithwall, was actually a traitor who told the empire about your plans to recover the Dawn Shard. So when you exit the Tomb you are met with a fleet of airships and Judge Ghis, forcing you to hand over the Dawn Shard that you just spent the last three hours of gameplay fighting to get.
And then you get a double dose of it later on. Cid taunts you by revealing his plan to travel to Giruvegan, but once you fight through all the baddies you find out that he never bothered to turn up, and tricked you into travelling to Giruvegan so that you could retrieve the Treaty Blade for him. Which is bad enough already, except that...
At Giruvegan you discover that the lost race who live there have been secretly manipulating one of your party members all along, and they give her the Treaty Blade so they can travel to Ridorina - which is where Cid is waiting for them to deliver the blade - because they want her to defeat him and use the blade to create an even more powerful McGuffin which will put the human race back in its place. So yeah, definitely one of the "90%" versions of this trope.
World of Warcraft has an interesting version of this during the Lich King encounter: After getting him to 10%, he instantly kills the entire raid and reveals his plan to let Fordring assemble the world's greatest warriors (the players), kill them, and resurrect them to form an unstoppable army. The entire fight against him was just a test, to see if they were worthy.
In Cataclysm, you're helping the game's Captain Ersatz of Indiana Jones to search for a valuable artifact. This being a massive Indiana Jones reference, of course his nemesis shows up to claim the artifact for himself. Subverted when the artifact bites back a la Raiders, thanks mainly to the timely intervention of famous explorer and archaeologist Brann Bronzebeard.
In Secret of Mana, the heroes are asked to retrieve the stolen Water Seed. They go to the underground tunnel, fight a boss, get hold of the Seed and bring it back to the Water Palace. Too bad Geshtar is there waiting for them, and the Seed gets stolen again.
In Drake's Fortune, the bad guys steal Drake's treasure map (which he spent his entire adult life searching for), but are too stupid to figure out anything else. Drake follows them to the island, where he eventually finds a more precise map - which they steal as well.
In Among Thieves, Drake wouldn't even be involved except the bad guys keep sending him to fetch stuff. Flynn "helps" Drake steal the first treasure map, waits for him to decipher it, then strands him for the cops. He spends three months in a Turkish prison for his trouble. When he gets out, he goes chasing after the bad guys to steal back the treasure. The bad guys are so stupid that he finds another map in less than three minutes - and the bad guys take it from him and try to kill him. He escapes and finds a third map - and they try to kill him again. When they catch him again after he finds another clue, they've figured out that they need him to finally get to the MacGuffin, and offer him a Sadistic Choice - and try to kill him again once he helps them again.
At one point the Big Bad gets pissed at Flynn's performance, pointing out that Drake has been one step ahead of them most of the time. He even wonders if he should have just hired Drake in the first place.
In Drake's Deception, the bad guys don't even bother looking for anything. They just follow Drake around and steal his plot coupons. He eventually wises up and, upon finding a star-based map, doesn't write down in his journal to be stolen, instead relying on Sully's knowledge to find the location. Surprise, surprise: Sully gets kidnapped. At one point, Elena attempts to talk Drake out of his quest, pointing out that the bad guys wouldn't even have gotten this far if it not for him. He brushes it off.
This part has more Unfortunate Implications than all the Mooks Drake wastes combined - the mooks in each game belong to a different Gang of Hats, so that's understandable. What's not so understandable is that they need Drake to find all the clues for them. "They are just uneducated thugs who need an American to work hard so they can steal from him."
One vital document was actually hidden in the bad guys' secret lair. It had presumably been there for decades without them noticing and yet Drake found it within a minute or two .
In The Legend of Zelda: Ocarina of Time Ganondorf pulls one, when he storms into the Temple of Time just as Link has gotten all of the Spiritual Stones, played the Song of Time on the Ocarina of Time, and grabbed the Master Sword. Turns out that Ganondorf had been following Link the whole time so the kid could do all the dirty work and the 'pure of heart' junk for him. After the Time Skip, he does it again. This time the Macguffins are the Triforce pieces of Wisdom and Courage that Zelda and Link possess. He captures Zelda the moment she removes her disguise and challenges Link to rescue her.
And in Twilight Princess, Zant does the same thing by taking the Fused Shadow pieces that Link and Midna have just spent the last forever collecting.
In Monkey Island 2: LeChuck's Revenge, Guybrush spends more than half the game collecting four map pieces to the legendary treasure of Big Whoop, only for the two bad guys LeChuck and Largo (who twiddled their thumbs the whole time whilst Guybrush was out retrieving the map pieces) snatch it off the cartographer he leaves it with.
BioShock has the end-of-second-act plot twist where Andrew Ryan shows that the player was being mind-controlled into doing Atlas' bidding through the whole game, and orders the player to kill himself, after which he pilfers Ryan's body and delivers the Genetic Key to Atlas, who reveals himself as Frank Fontaine, Ryan's biggest rival.
Legacy of Kain uses a variant of this, where Raziel plays right into the Hylden's hands by resurrecting the ancient vampire Janos Audron for the Hylden Lord to use as a host, and even murders Kain, the Scion of Balance, in the process. Take your pick on which is the proper MacGuffin: The Heart of Darkness, which had been used to resurrect Kain, or Janos himself.
Pulled off in the last game of Kirby Super Star, "Milky Way Wishes." The sun and moon begin to fight, throwing Popstar's day-night cycles out of balance. Marx, an adorable jester, tells Kirby that in order to make peace between the sun and the moon, he must ask the wish-granting comet Nova, who can only be summoned once he collects the power from all the neighboring planets. This was all Marx's plan. He was the one who tricked the sun and moon into fighting, knowing that Kirby would try to solve the problem by doing all the dirty work for him and summoning Nova. Once Kirby does summon Nova, Marx knocks him aside before he can make a wish, then wishes to control Popstar.
A variation occurs in Mario & Luigi: Superstar Saga. The brothers are racing to find the legendary Chuckola Reserve soda to cure Queen Bean, but the self-proclaimed "shadow thief" Popple also wants to get his hands on it. At one point in the forest, the Bros. have to use their new Hammer techniques to get three Chuckola fruits to pass a guardian. Once the Bros. get all three, the guardian lets them pass... at which point Popple and Co. come out of the bushes, enthused about how, since they couldn't get through the gate, their plan to wait for someone else to come and open it worked! The Bros. are not amused.
There's a minor attempted example in Baldur's Gate II: Shadows of Amn in Firkraag's lair, where some tomb raiders try to trick you into doing their dirty work and then kill you. Of course, it doesn't work.
In the main plot, you end up delivering a very important Macguffin to the Big Bad without realizing it until it's too late: your own divine soul. It stops being a Macguffin the moment you lose it, since the power it grants the Big Bad is made all too obvious. Worse, the loss of it grants you new and terrifying powers since your soul was the only thing keeping the essence of Murder at bay.
In Tales of Symphonia, Lloyd and his friends end up playing this role during the Journey of Salvation, when they end up powering the MacGuffin (Colette) and unwittingly hand it right over to The Dragon (luckily, Yuan intervenes). They end up doing the exact same thing again when they cure Colette's crystallization sickness only to ill-advisedly attack the Big Bad's lair, who was of course expecting them and instantly recaptures Colette.
Dead Island has you doing this for a whopping 96% of the game (as noted by the fact that when you get betrayed by the mysterious voice, your main plot progress is at 96%.) Since you're immune from zombification for some reason, the voice guides you to all sorts of venues before finally guiding you to a lab where scientists are working on a zombie antidote. When it's complete, the voice tells you to meet him on a prison island where you have to do some favors for prisoners before getting access to him. Once you finally meet he hits you with sleeping gas, steals the antidote, and calls in an order to nuke the island.
In Mass Effect 3, a mission on the Asari homeworld of Thessia has Commander Shepard activate the Prothean VI in their temple only to lose the fight against Cerberus assasin Kai Leng, and have it taken away by him.
This happens between two villains in Kingdom Hearts. In the prequel, Master Xehanort tells Maleficent about the other worlds and the seven Princesses of Heart in exchange for a favor. Cut to the first game in the series: after ten years, Maleficent has managed to hunt down the Princesses and get them in one place. Xehanort swans back onto the scene and takes over, with the added sting that he's in a different body and might not even remember their meeting.
In Dark Parables: The Red Riding Hood Sisters, the Wolf Queen needs Moon Essence, which is sealed inside the shrine of the moon goddess. Only the Elder Sister, who leads the Red Riding Hood Sisters, can access this; however, in light of current circumstances, the detective is permitted to do so instead. So the Wolf Queen just waits while the detective does all the work, then takes the element.
The villain in League of Light: Dark Omens tricked the main character into spending most of the game retrieving the special key needed to open the throne room where the Dark Lord's body had been sealed by the hero who last defeated him.
Devil May Cry 2013 actually inverts this. When Kat gets kidnapped, Dante goes on a mission to kidnap Mundus's mistress (who is pregnant with his child.) Once that's overwith, they agree to a hostage exchange. In the middle of the exchange, Vergil shoots and kills the mistress and the child while saving Kat, and gets clean away with Dante's help. To top it off, the time that Kat spent kidnapped proves instrumental to finding Mundus's security systems and overriding them.
The ending of Wario Land: Super Mario Land 3 sees Wario finally uncovering the Princess Peach statue underneath Syrup Castle, only for Mario to fly in with his helicopter and airlift the statue away.
Inverted in the webcomicAdventurers!, where the heroes were tasked with collecting the elemental artifacts. Their enemy, Rio the thief, was ordered to steal one of the elemental artifacts so that they couldn't, but in typical Rio incompetence, he stole the one artifact that had previously been successfully kept away from them. Shortly after, he confronted Drecker, who proceeded to steal it from him, resulting in the heroes' success.
Played straight when the heroes finally reach the end of a dungeon, only to have Khirma show up and take the crystal they were trying to keep from him.
A bit literally in The Fourth. First, Lord Skärva sends his minions to acquire a flower for use in a potion; second, the hero Blank confronts Skärva only to find the items he'd collected in the dungeons were food from Skärva's pantry, which he promptly put back there.
Tarquin: In any race for hidden treasure, it is always the protagonists who sweat and bleed and die to overcome the many challenges inherent in finding it—only for the antagonists to seize it from them at the last minute.
In the KateModern episode "Seven Dials: 5pm - 23rd November 2007", Charlie emerges from a building carrying the software, with Terrence in pursuit, only to meet the Watcher, who beats up both of them and drives off with the software.
Happens often in Jackie Chan Adventures. In fact, all seasons end with the villain getting what they wanted, but of course they still lose to the heroes. Both sides constantly run into each other throughout the series. Even Valmont pointed out how it was sometimes easier to have Jackie do the work for him of getting the MacGuffin.
An interesting variant happens in the season four where the heroes and villains race to collect the masks that contain the spirits of Tarakudo's generals. In the end, it does not matter which faction collects all the mask as long as they are collected together, making this Failure Is the Only Option as far as preventing Tarakudo from rising again is concerned.
Happens in an episode of Beast Wars. Rattrap, at great risk, dives to the sunken Axalon to retrieve the Sentinel control module - only for the Predacons to blast him and swipe it when he gets to the surface. It changes hands a couple more times before the episode ends, but the ending isn't happy.
In Kim Possible, "Monkey Fist Strikes" has Kim go through numerous death traps to retrieve a monkey idol in what may have been a Shout-Out to Indiana Jones, but that night, a ninja creeps into the camp and stole it. Of course, the ninja did turn out to be the masquerading villain all along.
In "Hidden Talents", Drakken fakes messages from Wade in order to manipulate Kim into stealing one of Professor Dementor's inventions and bringing it to him.
Subverted in Disney's Aladdin, Aladdin fetches the lamp and, lo and behold, the Big Bad Jafar is waiting at the entrance to the Cave of Wonders and snatches the lamp, double-crossing Aladdin and shoving him back into the collapsing cave. Later, it is shown that during the chaos, Aladdin's monkey stole the lamp back from Jafar before they were shoved in. After this point, the Lamp ceases to be a MacGuffin as its specific powers become central to the plot.
The use of this trope is one of the things taken from the Persian folktale the cartoon is based on.