After defeating Cagnazzo, the party becomes trapped in a corridor as the walls start to close in on them. They can't escape because the wooden doors are locked. You'd Expect: Since the party has not one, but TWO members capable of using Black Magic, at least one of them would think to destroy the doors so they could escape. Or, you know, simply TELEPORT THE PARTY FROM CASTLE BARON ALTOGETHER. Instead: Palom and Porom petrify themselves to stop the walls from closing in.
Cecil procures the Crystal of Earth in exchange for Rosa's safety. When confronting Golbez on the Tower of Zot to actually make the exchange... You'd Expect: Seeing that Golbez hasn't exactly shown himself to be trustworthy — if nothing else, instead of making the exchange outright he makes you climb his tower full of dangerous enemies first — that Cecil would insist Golbez either give him Rosa first, agree to make the trade at the same time, or at the very least make sure Rosa is physically present during the exchange. Instead: Cecil hands over the crystal immediately, and is surprised when Golbez responds to his demand for Rosa with "Rosa, who's that?"
The party is getting ready to travel to the moon on their Cool Starship. After numerous fights and trials, the party is finally ready to take down the Big Bad. You'd Expect: Cecil to maybe say a few words of encouragement and get down to business with his trusted and capable allies. Instead: Cecil orders Rosa and Rydia off the ship claiming it's "too dangerous" because they're girls and all. Rosa and Rydia happen to be the party's primary healer, and an obscenely powerful Summoner who can conjure a dragon to melt faces. They are the two most essential members of the party, with Cecil and Edge, the two claiming they should stay behind arguably being the most expendable. The girls have to resort to sneaking aboard the ship as it takes off in order to save Cecil from his own misogynist stupidity.
In Final Fantasy V, one of the four Warriors of Dawn, a werewolf named Kelgar, decides to challenge Bartz over a misunderstanding. You'd Expect: Kelger to actually stop and listen to what Galuf is trying to say and, once explained, tone down the machismo a little because he's way past his prime. Or: Bartz to not hit him as hard as he possibly can. Instead:: They insist on fighting over the objections of the other party members and Bartz wallops Kelgar so hard he's bedridden. And then dies a short while later.
The Ancients create a world-destroying object which, if used, summons a giant meteor to come and destroy the Planet. However, they need a way to keep this object from falling into the wrong hands, because if it did, said evildoer could use it to... summon a giant meteor to come and destroy the Planet. You'd expect: They wouldn't make such a thing in the first place, since it has no apparent productive use. Instead: They make their entire temple itself the world-destroying object, and as a security measure, design it so that anyone who activates the mechanism to shrink the temple down to usable size gets crushed inside. Because villains never have minions that they consider expendable and likewise, if the right hands come by, the mechanism tries to kill them anyway. Also: It is revealed in one of the later compilation works that the Planet has a mechanism for taking the lifestream and sending it to space as a last-ditch effort to save itself, so Meteor isn't as self-destructive as it seems at first.
The party actually manages to get the world-destroying object back from the villain before he is able to use it. Cloud, having figured out by now that he shouldn't be the one holding onto the thing, gives it to another party member, with instructions that he shouldn't give it to anyone, no matter what. You'd expect: This order would be interpreted as "Don't give it to anyone for any reason, *especially me*." Especially since there is no reason at all why the main character would ever need the thing for anything. It's an albatross, and the only reason the party is hanging onto it is to keep Sephiroth from getting his hands on it. Instead: The main character predictably falls under the villain's mind control again and casually asks for the world-destroying object back, which is quickly and cheerfully given. He then gives it to the villain, who promptly summons the giant meteor to destroy the world. ...while the Shinra goons that have been chasing them through the whole game are standing RIGHT THERE!!
A lesser act of stupidity, but extremely blatant nonetheless. At Wall Market, Cloud and the girls finish "interrogating" Don Corneo and are on their way out. Corneo asks them to wait a second. You'd expect: Cloud and the others to just keep walking. Getting that intel was the only reason Tifa went to Corneo in the first place, and Cloud and Aeris were only there for her. Now that they have it, they have no reason to stick around and a very big reason to get to Sector 7 immediately. Instead: Cloud stops in his tracks and hangs around long enough for Corneo to drop the trio into a trap door. The time spent fighting Aps and then going through the sewers and the train graveyard could have been better spent saving Biggs, Wedge, and Jessie, and getting to the top of the control pillar in time to throw Reno off before he could tamper with the controls. Smooth moves, spiky-haired boy.
Rinoa comes up with plan to neutralize Sorceress Edea's powers during an important military mission being run by her father; a plan that's well meaning but so poorly thought out that Quistis even laughs at it. Rinoa is then told that this is Not a Game and that she should stay where she is. You'd expect: Rinoa to either do as she's told or (more likely) make an argument as to why this plan could work during this particular time. Instead: She decides to be rebellious and go to the sorceress ALONE so that she can put the neutralizing bracelet on her herself. She does this right before her dad locks the door to her room and Quistis, Zell, and Selphie come in due to Quistis getting her turn to hold the Idiot Ball. Once Rinoa manages to reach the sorceress and enact her plan, it's clear she has no idea what she's even doing.
After Quistis shoots down Rinoa's aforementioned plan and then relocates her team to the gate where they'll be stationed during the very important mission, she feels sorry for what she said, and wants to go back and apologize. You'd expect: Quistis to realize that she can't abandon her position during a mission just for a personal issue, and that the apology can wait until it's over. Or she leaves her teammates and heads back alone (how many people does it take to throw a switch?) Or she sends Zell or Selphie to apologize for her. Instead: They all run back together, get locked in, and only get back in position in the nick of time thanks to a serendipitous hidden passage into the sewers.
Final Fantasy X: At one point, Rikku - aiding the party's escape - produces a flash grenade and yells "Cover your eyes!" as she tosses it at the villains. You'd Expect: Everyone in the immediate vicinity to cover their eyes, as instructed (including the villains, who are normally intelligent enough to know they should probably listen to the Al Bhed girl tossing bombs). Instead: Seymour grabs the Villain Ball and stares straight at the bomb at his feet for a good two seconds before it goes off.
Final Fantasy XII: Judge Ghis manages to extort the Dawn Shard, a piece of deifaced nethicite, out of the party's possession and sends them on their way. The Archadian Empire, who he serves, has the Midlight Shard as their basis for their own manufacturing of nethicite, and the Dusk Shard which they got off of Vaan in an earlier event. So he should know very well what it can do. He also got a demonstration as one of his spells was cancelled when he tried to off the party via You Have Outlived Your Usefulness. You'd expect: Judge Ghis to just fly the Leviathan straight back to Archades with it in tow. Instead: He hooks it up to his ship's engines to see what kind of power it possessed. It does two things... (A) It drives Fran completely berserk, and she tears through Vossler's forces before the party has to step in to shut him down. This is the less significant effect, for reasons soon to be painfully obvious. (B) It siphons all the power from the ship's engines in record time. The party escapes aboard the Shiva before everything goes straight to shit, with both the Leviathan and the entire fleet accompanying it being decimated in the equivalent of a thermonuclear blast. Some things just shouldn't be fucked with, but I don't think he cares anymore, what with him being dead and all.
Final Fantasy XIII-2 has Caius making an attack to provoke Noel to kill him. You'd Expect: Noel will just drop his sword to prove his point of not wanting to kill. Instead: He puts his sword nearly at his chest. Since he won't do it, Caius just grab his hand to stab himself with it.