It's no surprise that Barty Crouch Jr. was able to have enough polyjuice potion to last him all year. There are golden polyjuice potion cauldrons scattered all over the school.
A great idea for a cutscene after the 2nd task would’ve been Snape asking Harry about the theft of some of his potion ingredients and assuming he and his friends were brewing Polyjuice Potion (a few golden cauldrons throughout Hogwarts are then shown). Harry pretends to be oblivious about it.
In the Wii version of Years 1-4, there's a glitch where if you get all 200 golden bricks and play the bonus level, you're not allowed back into Hogwarts and are taken to Knockturn Alley instead. This may seem annoying, but if you think about it, the game is pretty much saying that you are officially done with Year 4 and need to move on to Year 5 in the next game.
Why aren't you allowed to enter areas in Year 5 you were once allowed to enter previously? Yes, it's a new game, but also Umbridge most likely reblocked those doors as part of her series of restrictions.
In Philosopher's Stone there's a segment where Ron or Harry have to pretend to be a girl to get into the girl's bathroom to save Hermione from the troll by using wig. On paper this seems like a Paper-Thin Disguise (and is indeed referred to as such in the main page) but then you remember that they're 11, pretending to be a prepubescent girl (case in point Hermione is prepubescent for both the first and second film), and at that age a long haired boy could easily be mistaken for a girl.
Why do all of the objects Arthur Weasely repairs function very differently to how you'd expect? Because it's Arthur, who loves to experiment with Muggle objects and likely doesn't understand how most of them actually work beyond their purpose. "What is the precise function of a rubber duck" indeed.
Why is it that in the Dragons! level of Years 1-4, you need to perform a musical puzzle to bypass the Welsh Green dragon? Because in Fantastic Beasts and Where to Find Them (the book), the Welsh Green is described as having a "melodious roar." They tied the game to Harry Potter canon not mentioned in the main series!
A collectible type is "students in peril". No one seems to care about them, no one notices them, even the ones that are in plain sight. Some just need to get something down or have a missing object, but what about the ones that are caught in devils snare or locked in the cupboard when the dragons destroying the towers?
Even when you know a student is trapped, you are powerless to help them until you get the right ability. In-universe, this can be years later.
Not to mention, some of the areas students are trapped in are a bit questionable, including one trapped in the tent (making very distracting grunting noises), one trapped in the Dursley's shed, one trapped at the bottom of the Black Lake under a boat, and one being practically waterboarded by another student. I didn't even get to the ones trapped in the dungeons.
