The game has escort missions, which are already widely hated by pretty much everyone. It wasn't so bad early on, defending thermobaric tanks and such, but the escort mission immediately before Elizabeth Greene's boss fight would likely cause broken controllers. One pump vehicle pumping BloodTox veeeery slowly and wave upon wave of Leader Hunters who just sprint straight for it and smack it with AoE's until there's not even a bolt left. Wonderful.
The racing side missions, where the player has to move through a variety of waypoints in order, under a particular par time. Fair enough on its own, but the mechanics of the player movement tend toward going very fast, but also being very imprecise. Moving through a tiny waypoint when you overshot your target because you were moving too quickly feels like Fake Difficulty.
In ActRaiser your god avatar has a set number of spells per level attempt. That's right, not per life, per level attempt- you don't get your magic back when you die. If you use all your magic against a boss but just fail to defeat it, then your only choices are to work out a way to beat it without magic or to lose all your lives and start the level from the beginning again. Although the unresponsive controls and mediocre collision detection were pretty bad problems, the magic issue stuck out as both clearly deliberate and plain mystifying.
Worse, you had to manually equip spells through a fairly terrible interface before going into the level, every single time.
Ōkami has the digging minigame. It is a timed event which requires you to dig by using your brush powers to remove certain obstacles while you escort a companion whose life mission it seems is to walk into every time reducing object possible. Add to this that on the Wii version, the brush controls only work half the time. Also, certain actions such as blowing your companion over gaps or shooting them up with water spouts only work if your timing is absolutely dead on, and even then he will tend to walk right off the edge you just popped him up on, making you start again. Thankfully, there's only two times it's necessary and they're the easiest ones.
And even worse, drawing lightning bolts. And it's extremely hard to aim them.
Ōkamiden has its own, which is both simpler and far more pervasive: Ink doesn't regenerate if you picked Old Hand way, back on the title screen, which is the game's Hard Mode. This will cause you an enormous amount of pain during certain boss fights, particularly King Fury. It doesn't help that because of the difficulty names (Greenhorn and Old Hand), it's an easy mistake to think they're asking if you want a tutorial, but it's actually a difficulty select. If you chose Greenhorn, ink DOES regenerate, but only after you've run out of ink, making this not so much a scrappy mechanic as an added challenge. The real mechanic is the aforementioned not realizing it's a difficulty select in the first place.
As the page image so eloquently illustrates, the vanishing blocks that are found in nearly every single game are utterly despised by gamers. Even the sound they make pisses retro gamers off to this very day.
Mega Man 8: replaced the blocks with the jetboard in Frost Man's stage and Wily's Castle. It's evenworse. They added a flying drone whose whole purpose is to yell out commands to get through the jetboard gauntlet, because they didn't think the player could manage it on their own. And just to make it absolutely perfect, the voice is infuriating and interrupts itself.
The Game Boy games, Mega Man 7, Mega Man 8 forced you to beat four of the robot masters first before you could go after the next four. Mega Man & Bass took this Up to Eleven with an odd system that unlocked new stages depending on which ones you beat prior. Saying this mechanic was unpopular would be an understatement.
The Mega Man Homepage: (On 8) Once again, you must tackle four Robot Masters at a time. (Why does Capcom keep doing this?)
The removal of charging and sliding in Mega Man 9 and 10 is a bit controversial, with some not appreciating the removal of long-standing mechanics to make the games more like Mega Man 2.
Ride Chaser levels (X4 and X5 especially). Walls that block you come out of nowhere, the damn things aren't very responsive anyway, and maybe a second to respond to changing terrain, bottomless pits, and the aforementioned walls. Significantly less scrappy in X8, but still annoying.
The Ride Armor sequence in X5 (Mattrex's stage, part 2) could be avoided, and good thing, because it's built around the fact that the Ride Armor can withstand the lava (whereas the also-robotic main characters cannot). You take the Ride Armor (and its not-displayed health bar) deep into the lava itself, and if it gets destroyed, you die and go back to the beginning. The sequence ends with having to ditch the Ride Armor in the lava; you have to jump and eject yourself from the Ride Armor (hold "Up" and press the jump button) at the peak of that first jump. The slightest slip-up kills you and sends you back to the beginning. Considering that the route you can take to avoid this is a Shout-Out to Mega Man 2, and this is the only level in X5 that the Ride Armor appears in, why is the Ride Armor here at all?
There's also Zero's "nosedive" attack in X6 that's activated by pressing "up" and "attack" at the same time. There's also the fact that the "Up" button is used to grab ropes as well. If you're in the habit of holding "Up" when jumping along horizontal ropes situated over spike pits and whatnot, a single enemy in your path can make you accidentally trigger Zero's diving attack, sending you back to whatever obscenely-placed checkpoint you're forced back to. Even worse, for the Anniversary Collection, the developers were planning on changing the controls for the attack to prevent the above issues from happening, but they were barred thanks to the existence of the Maverick Hunter X game; yes, because they were expecting to build a series out of it, and change the controls when they got to that game, the Anniversary Collection version of X6 got gypped out of having this particular scrappy mechanic taken out. What?!
X5 had random Reploids in a few levels, who were meant to be hostages and could be rescued simply by touching them, as they reward you with an extra life and a (usually minor) health refill. This was their only use, and in a game where you get unlimited continues anyway, their helpfulness was a little questionable. Altogether, though, not too scrappy. X6 put sixteen of these hostage Reploids in each level, and some of them give you upgrades with no in-level indication of who gives what--or indeed, anything. That's... annoying. X6 also introduced these Goddamn Bats called Nightmares (the floating tentacled things that drop souls required to use the aforementioned upgrades on a character, in itself another Scrappy Mechanic). They can fly through walls, commonly appear in packs, can revive themselves if you don't pick up the souls they drop, and...oh yeah, they can possess and disfigure the hostage Reploids, sometimes even ones that are offscreen. Needless to say, any hostage that gets possessed and has to be destroyed never comes back, making any upgrades they may have had Lost Forever.
X6 flip-flopped a little on the subject of how easy it should be to thwart a Nightmare from possessing a hostage. On one hand, any hostage within range would draw the Nightmare's undivided attention, and you could shoot them in the back as they slowly flew toward the hostage if you were feeling that risky. On the other hand, some Nightmares are very cruelly placed, to the point where one Nightmare in particular is directly on top of a hostage Reploid.Yes, this means you could lose a Reploid before you can even see him.
The Nightmare System in X6 would cause changes to certain levels if you went there from a certain other level. The levels in X6 are aggravating enough, but certain Nightmare System changes could render them nigh-Unwinnable (good luck trying to get past the first avalanche section in Blizzard Wolfang's level with X/Zero copies attacking you constantly.)
X7 would have been bad enough even if its targeting system worked as intended.
The ranking system in the Mega Man Zero series. In Mega Man Zero 2 and 3, you HAVE to have at least an A rank in a stage to obtain a special weapon from the boss. To get high ranks, you must go through the stage quickly, taking little damage and defeating many enemies. Yes, all of those at once. Zero 4's special weapons depended on another factor unrelated to the ranking system and were therefore much easier to get, but the game then introduced, if anything, an even Scrappier Mechanic: item recipes. By putting together specific combinations of chips dropped by enemies, you could make powerups that let Zero double-jump, walk on spikes, charge up faster, etc. The problem is, you have no way of knowing whether or not any particular combination will actually do anything until you put them together, aside from a few recipes that can actually be received in the game. You'll just have to use trial and error for most of them, and doing that will use up those chips. Heaven help you if you tried that with one of the chips dropped by an enemy that only appears in one of the non-revisitable stages. And of course, there's no indication in the game of how many recipes there are either...or even how many chips you need for any of them (given that they can require anywhere from 2 to 4). Combine Guide Dang It, Trial-and-Error Gameplay, and potential Lost Forever and you have an incredibly frustrating gameplay mechanic.
Cyber-Elves were a pretty nifty and fairly heavily advertised addition to the Zero series, granting all kinds of special abilities. Except that the game punishes you for using them by placing a permanent penalty on your rankings. Later games would only have a few Cyber-Elves that penalized you, and Zero 4 changed the system entirely by giving you only one Cyber-Elf that you can upgrade and downgrade as much as you want, and you only get penalized for making her too powerful (and the limit is raised continuously as you progress through the game.)
Mega Man Legends gave you a digger's license which served to Railroad you in the direction of the plot and would be upgraded as the story progressed. The sequel decided to instead make you take a Digger's Exam: A timed level with a very strict time limit with a weapon loadout that pushed you about as close to a No-Gear Level as the game could get, making for a mind-numbingly difficult run. Not only were the tests mandatorynote While you could take them early, sooner or later you'd reach a mandatory to explore ruin that was above your grade, but all the enemies in every ruin upgraded to more powerful versions of themselves every time you passed an exam.
Some of the best equipment and rune words in Diablo II were restricted to players on the ladder, a harder version of the game on Battle.net with a finite amount of time to find the ladder-only itemsnote Every 6 or so months, the ladder resets. All ladder characters from that season are permanently booted and lose the ability to find ladder-only items but get to keep whatever they found. Players who wanted a slower-paced game, preferred single-player, or didn't have reliable Internet access were out of luck.
Likewise, the kayak in Tomb Raider 3. Vehicle sections are welcome most of the time, but the kayak handles just a little too realistically to be fun having to navigate lethal rapids and waterfalls full of deathtraps with. There were some points with the kayak where it was impossible to proceed without taking heavy damage from the traps and falls.
The tightrope walk sections in Tomb Raider Chronicles would count too. Lara can easily fall off if you fail to regain her balance and crossing is sometimes based on luck. Since Lara losing her balance is randomized, you could wind up spending more time readjusting than actual tightrope walking.
Lara losing her balance or grip in Tomb Raider Anniversary is, on paper, a mechanic where sometimes she slips when grabbing a ledge or balancing on a pillar and you have to press a button to steady herself before she falls. In practice, it turns every single "time your jumps to avoid moving blades, crushing walls, etc" segment into a Luck-Based Mission since, if she happens to lose her grip or balance, you will be hit by the obstacle and killed before you can act.
The poison mechanic in Tomb Raider III and The Last Revelation. Once you were poisoned, you'd gradually lose health and the only way to cure it was by using your vital health kits. What made this worse was most enemies that could poison you either traveled in groups or were hidden from view.
The original Metroid features a punitive health system wherein, no matter how many energy tanks you had when you died, you start back off with 30 health units. Want another chance at the thing you died at? Better spend time laboriously farming enemies for 5-point health units. Later titles in the series wisely kicked this mechanic to the curb without a second thought.
The game has an infamous Wall Jump, which requires the player to roll-jump towards a wall and hit the opposite direction on the control pad, before pressing the jump button a millisecond later. This takes hours to perfect and is needed to escape a certain area, and to collect all the powerups.
The Shinespark jump allows Samus to store energy from the Speed Booster and use it to make a super-jump. It was a difficult but manageable technique that wasn't used very much. Using it, however, damages you over time, so you better be careful that your health isn't low enough (this was fixed for the GBA games, but... well, see below). Another thing scrappy about it is how the move is done: you need to be in midair to use it, the diagonal version required you to use one of the shoulder buttons to perform it and there was a high chance that either the horizontal or diagonal version would come out as the vertical version instead. In later games, all you need to do after storing energy is hit jump and hold the direction you wish to travel in.
Thanks to the button architecture of the Game Boy Advance, the Speed Booster in Metroid: Fusion and Metroid: Zero Mission isn't activated with a run button, and instead activates after running continuously for a few seconds. This means if you don't expect Speed Booster blocks to be up ahead, you're going to have to (rather slowly) backtrack a short distance and spend those few seconds building up the Speed Booster to progress, bringing the pace to a screeching halt. Even worse is that someone on the development team must have loved the Shinespark a bit too much and made it come into play far more often than in Super Metroid, so if you want 100% Completion, you're going to have to build up the Speed Booster and use the Shinespark aLOT, and some rooms make you do it again if you screw up. After backtracking back and forth across two or three rooms trying to get that Missile Tank for the thirtieth time, you'll be begging for the GBA to have one extra button just so that it could be used as a run button to speed the process up.
The main three games have a controversial implementation of a scavenger hunt toward the end. The first Prime isn't all that bad, since you can collect the required artifacts throughout the game, with only one unavailable until the endgame (and even then, it's only located two rooms away from the spot where the endgame really starts). In the second game, however, you must have the Dark Visor to begin acquiring the keys — a few also require the Light Suit, which is approximately 95% of the way through the game (and you need to scan the slots where the Keys should be placed, or else their lore entries will be Lost Forever). The third game has a better-implemented scavenger hunt with the Energy Cells, as you don't need all of the Cells to complete the game and some are gotten automatically as you progress normally; also, a simple speed trick on the Valhalla allows you to skip two more cells in the Aurora Chamber; if you're just looking for bare-bones completion, you needn't go out of your way at all for Corruption's scavenger hunt.
Echoes also has the ammo system, which is a conventional gameplay device for most first-person shooters, but not for a Metroid game. The fact that the Light and Dark Beams have a finite amount of ammo (which can be increased with ammo expansions) means that players have to balance the use of both as it's the only way enemies will drop ammo supplies when they're defeated. It's made worse in the case of the Missile Combo powerups, because they need 30 ammo of a particular type in addition to 5 Missiles per shot (in the case of the Sonic Boom, it requires 5 Missiles, 30 from Light Beam and 30 from Dark Beam per shot). Fans didn't like this mechanic, so it was ditched in Corruption.
Even Metroid hacks have been known to imitate the Prime series' scavenger hunts. Super Metroid Redesign sends you in search of twelve well-hidden Chozo guardians, some of which are inaccessible until the right conditions obtain. The worst is a tube in Maridia which, unlike all other tubes of that design, can't be broken by Power Bombs; instead, it breaks when you defeat Ridley (halfway across the planet).
While it wisely stowed away with the idea of a third-act scavenger hunt, it introduced the Concentration-based health system. In every other Metroid game, enemies would drop health (and missile) boosts when you killed them, keeping you topped up on-the-go. Other M does away with this completely; the ONLY ways to restore your health at all are through save stations (which function here as recharge rooms as well, similar to those in the Chozo Ruins and Mothership in Zero Mission), and through a new technique called Concentration. At any time, you can point your Wii remote upwards and hold A to replenish your missiles fully, but with health it's trickier: you can only restore health when you're so low that a few more hits will kill you, and to do it you need to perform the technique while standing still and unable to defend yourself for a few seconds. Now, where are you most likely to run your health low enough to be allowed to use this technique? In heated battles where the enemy won't exactly sit around while you're trying to heal. And even then, it only gives back 99 units of health at first - you can find upgrades that increase how much you can get back, but you need to go out of your way for them. It turns the entire game into a Nintendo Hard endurance test. Though, one supposed players should have expected something like this from the same development team that brought us such fair and reasonable entities as ALPHA-152.
Then you have the "Pixel Hunts". There are several scenes where the player is locked and immobilized in a first-person viewpoint until they spot some background detail. Unfortunately, such details were almost all extremely difficult to notice, from a splotch of green blood in a grassy area to a brown caterpillar in a dark brown room. These moments killed the flow of the game and often became a Guide Dang It. Worse still, the final boss is one of these, and can kill Samus in a matter of seconds.
In a broad sense, the "Authorization" mechanic, in which, instead of losing all upgrades at the start and gradually replacing them as time goes on, Samus gets the use of various aspects of her suit "authorized" over the course of the game. So expect to be trudging through deadly lava for a good fifteen minutes, before Mission Control finally allows you the environmental protection of the Varia Suit that you already have. The mechanic so flew in the face of basic logic, that the idea that Samus and her commanding officer are in an abusive relationship seemed to be the only logical explanation.
There was also the  that the missile mechanic introduced. Most of the game was in third person. In order to fire missile, one assumes a first person perspective. Yahztee adequately described it as feeling "as smooth and natural as deflecting bricks with your head while wearing another brick as an earring."
Aerial levels in Drakengard are, sadly, half the game. They start off all right, but then the enemies gain homing attacks. Every last one of the enemies, that is. You have homing shots yourself (albeit weaker than non-homing) and a magic-attack "bomb," but in order to gain all the weapons, you have to clear several aerial missions without using the magic attack and under strict time limits. It doesn't help that you can't "hover" (this was fixed in Drakengard 2), making aiming a game of luck, and that you turn so very slowly.
It is a fun little game about a small mech with a drill for arms. In certain circumstances, death will simply send you back to the start of the room with a little less health. If you lose a fight enough times, you're given the option to spend 50 "chips" to Continue. Otherwise, you're booted all the way back to the opening screen. Not even the menu, the cutscene you get when you boot up. And when you load your save, if you saved in a boss room, you have to sit through the entire pre-boss cutscene. Every. Single. Time.
There's also the Drill Missile. Inside are platforms with little electric orbs on them. Two different types, in fact; blue orbs that move at a steady pace, and pink ones, which move like they're on crack. There are also elevator platforms that flip over to reveal their electric underside. And it's timed. Fail the extremely precise timing challenge, and you get booted out and have to start the mission again. And you will.
Blast Corps has the Backlash, a dump truck. A clumsy drive combined with its unique method of building destruction (powersliding so its flatbed hits buildings) make every level where it's required a pain. It's also in the running for "most common vehicle in the game", and certainly has the most levels devoted to it.
Sadly, a big part of the gameplay of Fragile Dreams: Farewell Ruins of the Moon falls into this: The weapon you use can break at any time, you have a very limited capacity to carry things with you and to see certain objects you have to come back to a save point. The battle system is kind of scrappy too; even if there are different kinds of weapons and each of them has a decent selection the player is limitated for the whole game to a single combo. This is the reason why the game is more an emotional experience than a gaming one and therefore the player should specially focus on its story, characters, art and symbolism.
The day and night mechanic which many people hate, mostly because it makes everything take twice as many hits, the towns unsafe, and the slow-as-hell unskippable text box stating the obvious to pop up. The phrase "WHAT A HORRIBLE NIGHT TO HAVE A CURSE" will be drilled into your head forever by the time you complete the game.
The grinding to get hearts and running back to town just to get an item. And if you get a Game Over, you lose all of them!
The Magic Seals are a good example of how implementing a part of the system's capabilities isn't always a good idea. In order to finish off the boss, you have to draw a particular seal using the DS's stylus, or the boss regains a portion of their health. While simple at first, it gets frustrating as you're forced to use more complicated seals as well as less time to finish drawing the seals and most of the later bosses (Gergoth, Death and Abbadon in particular) are simply a nightmare to fight, particularly if you slip up. At least the bonus Julius mode didn't force this on the player again. The worst offender is Magic Seal 4. Due to a glitch, it won't cancel when player makes a mistake or runs out of time (the only way to cancel is to stop drawing seal), yet making the seal unfinishable upon either happening. It may take a while before player notices what's wrong.
Defeating the Balore boss gives you to Balore soul, which can only be used in six rooms in the entire game, including the room you found it in.
Castlevania: Portrait of Ruin features the Sisters mode, which has a set of controls completely unique from the other character modes; you use the D-pad to move your floating characters around and attack by touching where you want to attack with the touchscreen. Unfortunately, the developers neglected to allow movement with the four face buttons as well, making the game effectively unplayable for left-handed players.
Sly's "ledge jump". To elaborate, if you land on the very edge of a platform and jump, Sly will kick outward away from the platform. True you gain more air than a normal jump, but that's a moot point since it's much easier to use his paraglider for that. Most often you tend to activate it by mistake when you jump to a far ledge, making Sly jump blindly towards the camera and most likely into the Bottom Less Pit you just jumped over.
Murray missions in general. Since Murray lacks pretty much every sneaking skill of his allies, he's reduced to lumbering through levels and taking enemies on head-first. Because of this, he tends to get the crappy mini game levels such as the much abhorred Murray Games.
The Clue Bottles in the fourth game. The first game's linear levels made them fairly easy to find, but the sprawling areas in Thieves in Time make them absolutely miserable to track down even with a walkthrough. One of the obtainable bonus items, the Clockwerk Eye, alleviates this by marking the bottles on your mini-map, but you don't get it until well over halfway through the game, and to acquire it, you have to find all the clue bottles in one of the levels.
Also in Thieves in Time, one of the developers apparently loved the side-scrolling camera angle. Often when you try to make your way across a wire or a set of tricky jumps, the camera will re-orient to a side-scrolling perspective which roughly doubles the difficulty of said tricky jumps. It's particularly scrappy since if you actually wanted that camera angle, it would be very easy to just orient it that way yourself if the camera didn't abruptly jerk around.
Also in Thieves in Time are the controller-tilt mechanics that serve to stink up the otherwise fun hacking levels and contribute to the scrappiest part of the Murray Games mentioned above.
The Amazing Spider-Man 2 has the Hero/Menace meter. At first glance, it seems similar to those seen in other games, like Red Dead Redemption, but the way it's handled turns this from a promising mechanic to an annoying one. The game has side missions showing on the map for a few minutes, and completing them before they disappear makes the meter go to the "Hero" side. How does the meter go into the "Menace" side, you ask? Well, it has to be by committing acts of cruelty, like attacking civilians, or destroying property, right? Well, no. The meter goes down by not doing the side missions. That's right, you're called a "Menace" not by doing something wrong, but by failing to do a few more right things than all the ones you are constantly doing. Well, it's popularly known that Uncle Ben died due to Peter's inaction, so maybe the game design is simply enforcing the theme of responsibility. Alas; late in the game the number of side missions that show up is so large, that several of them will disappear at the same time. That means that you might be completing a side mission and your meter will still go down, since several missions disappeared in the time it took you to complete one, so even if Spider-Man is doing is best, he's still a "menace" because he's not preventing every crime in New York City at once. Note that the Hero/Menace meter is not just for decoration. If you go to the "Menace" side you'll be attacked by a task force, which will make your progress a chore. You'll be forced to grind a lot of the side-missions just to keep them from attacking you, and considering that every time you end one of them you're forced to hear a news report about it that gets old really fast, it will be extremely tiresome. Even worse is the fact that when you manage NOT to fight these guys you still have to deal with the electric nets that the Task Force puts up that prevent you from web slinging as effectively. It gets real tired real fast.
Those damned vanishing solar platforms will drive you bananas if you're actually playing the game fair and square in the sun rather than just cheating. They vanish if the solar gauge is less than three or greater than six, and keep in mind that falling off a cliff on this game is a straight-up Game Over rather than simply dropping you back at the entrance with some missing life. Expect to die, and die, and die just trying to get across that chasm.
The greatly reduced MP meter in the third game will become very frustrating in very short order. The first game gave you only the solar gun, and so you had upgradable batteries as your power source. Item space was ludicrous (99 of every individual item) and you could also swap in your old batteries for backup (A grand total of 15 full bars of energy). The sequel reduced this to a single MP meter and a 16 slot item cache, but also made using your magic optional since you got melee weapons instead. The third was a hybrid of this, giving you the gun but only one MP meter to go with it and the much more restrictive item system. You will be starving for a skylight or a solar nut every step of the way.
The game has Weapon Affinities, wherein each individual part grants bonuses or penalties to certain types of weapons. The problem? It's based off of what the mecha used in its home series, effectively limiting your builds to aping the source material. For example, the Zaku II has affinities for Machineguns, Bazookas, and Axes; if you want to use anything else, your damage output will plummet and you'll be forced to either suck it up or either waste valuable Module space on items to bolster your Affinities. When the sequel was announced, the removal of Weapon Affinities was one of the first improvements Bandai Namco mentioned.
In a lesser example, all parts had a star rating (from 0 to 10) which determined their overall stats and were Random Drops. This resulted in lots of grinding and lots of Vendor Trash, as well as inflicting Complacent Gaming Syndrome since everyone tended to pick parts from only the most powerful machines (like those of the Strike Freedom and 00 Gundam/Raiser). The sequel removes stars in favor of an Item Crafting system that lets players create and level parts as they choose, meaning that pretty much everything in the game can be viable if given enough work.
Chibi-Robo Park Patrol: Levels in the game are entered via a game of chance called the Wheel of Destiny. Before entering a stage the wheel is spun and the player will land in what ever level the wheel hits. There is no choice in what level the wheel will stop on so you can very easily land on the same level again and again, even after 100% completion of it. To top it off the pause menu lacks the option to quit the level even if it has been cleared. To be fair the game includes power-ups for the wheel to attempt to skew the wheel in their favor.
LEGO Adaptation Games have habit of dangling some minikits out of your reach after solving a puzzle. You can play levels in Story Mode or Free Play, and some minikits can only be found in Free Play as their puzzle requires a non-story Player Character. Others, however, the puzzle itself is quite solvable in Story Mode but then the reward minikit appears in a place where an ability like Double Jump is required to reach it... which your character lacks. Not only do you need to come back in Free Play to find it, but you need to do the puzzle all over again like a chump.
The Upgrade glitch in the Playstation 3 version. Every time you load a save the game "forgets" that you've unlocked any and all suit upgrades. The glitch is usually (keyword being "usually") fixable by accessing the Bat Computer and going to the upgrade menu, and thankfully the upgrades are optional and not required to finish the game, but still frustrating when you consider upgrades are your reward for finding the red bricks in hero mode.
Since Batgirl doesn't appear in Story Mode and has the same abilities as Batman the dev team decided to foist her on you in Free Play instead of Batman roughly 95% of the time. Unfortunately she controls more loosely and is cursed with the useless Wall Cling and Backflip moves. The former tends to activate accidentally when trying to jump to a ledge and the latter tends to activate accidentally during platforming segments, meaning you'll be falling into a lot of Bottomless Pits every step of the way. On the flipside Nightwing actually controls better than Robin and has the same abilities... and yet you almost never get to play as him.
Phoenotopia: The melee attack, the one that the player is relying on deal most of their damage, is agonizingly slow and only connects at the very end of the attack animation. This means there are a lot of enemies you need to maneuver onto level ground just to have the space to get your attack timings right. In particular, harpies need very finicky dodging and/or timing to land a hit.