Plot hole: Harry can now see the thestral creatures because he witnessed Cedric Diggory's death in "Goblet of Fire." However, he should have been able to see the thestrals after Professor Quirrell died from Harry's touch in "Philosopher's Stone". Quirrell crumbles into dust (dying) while Harry is still conscious, watching, and fully aware of what he is seeing, thus allowing it to fully sink into his consciousness. Harry faints "after" Quirrell is dead and as Voldemort's spirit passes through his body. Nor does it only have to be a friend or loved one who dies before the thestrals can be seen - it can be anyone, including an enemy like Quirrell. There only has to be an emotional response to the death, which can be love, hate, fear, shock, etc. (In the book, Harry did not see Quirrell die, but that's irrelevant to the film).
Suggested correction: JK Rowling has said that in order to be able to see thestrals the death has to "sink in" psychologically with the person. Which was her explanation for why he couldn't see thestrals even though he witnessed his mother's death. Given Harry's age and the way Quirrell died, it is possible that Quirrell's death didn't have enough of a psychological impact on him to "sink in." After I first personally witnessed a violent death, I didn't feel the impact until a few years later. It can take time.
Plot hole: When Jo is getting to walk down the aisle with Queen Clarisse, he hands Shades his top hat and then pops his ear piece right off, in a split second, and puts it in the top hat. In the previous scenes, Princess Mia has Lionel's ear piece stretched from the back of his neck, across his jaw and around his chin and then stretched to her ear but it hasn't popped out, while Queen Clarisse jerks Charlotte with her when she goes to listen to Princess Mia.
Plot hole: Although it is explained how the chipmunks were able to get away with the balloon race by tricking Ms. Miller, wouldn't Ms. Miller know that the chipettes were in on the balloon race? Especially considering the fact that she is their guardian? Also, why would she offer to babysit the chipmunks if she has chipettes to look after herself? Despite this, the chipettes were never brought along to Dave's house with Ms. Miller. And what is Ms. Miller still doing in Dave's house if she thinks the chipmunks are with Dave? Unless maybe she's taking care of the house...
Plot hole: They all drop their backpacks and bags 3/4 mile down into the hole before climbing by rope into the caverns to begin their journey. Later in the movie, they are all sitting deep in the caverns complaining about the lack of water supply. Suddenly the long-haired guy pulls out a large glass bottle of gin, completely intact and they all drink from it. There is no way his pack could have fallen 3/4 mile onto a hard surface without that bottle breaking.
Plot hole: In the scene where the Wicked Witch is furious because Dorothy and pals have been saved from the poppy field, the Flying Monkey hands her a golden cap. She then dashes the cap across the room. The golden cap is used in the book to summon the Flying Monkeys. They shot scenes involving use of the cap, edited them out, but left this one with the cap inexplicably being tossed about. (00:57:05)
Plot hole: After The Pie runs away and breaks the delivery cart, Velvet jumps on Miss Ada (the family's cart horse) to chase after him. It seems very convenient that Miss Ada, whose only job is to pull the cart, is standing untied in the yard wearing a riding bridle, just waiting for Velvet to jump on.
Plot hole: When 625 is activated, he has nothing with him, so how does he make all those sandwiches out of nothing?
Plot hole: The entourage of scammers travel about the city at will. One of the group is an internet junkie who always has his laptop in hand and turned on. No matter where they go, in their car, in an old warehouse, etc., they always have an uninterrupted wireless internet connection.
Plot hole: How could Pod have been sure that Pete would have all the things he needed, when he is preparing to rescue Peagreen from the milk bottle?
Plot hole: When we see the Zenith Team playing softball, it's a scene taken from later in the movie. For one thing, Mr. Pibb is there, even though we don't meet him until the next scene. Second, they're in the room with the UFO, but we don't see that until later. Finally, Zoom's outfit is different than the last scene, but in the next scene he's wearing the same outfit.
Plot hole: There is no way that 'coast of Iceland' could ever have been mistranslated as 'coast of Ireland'. For this to have happened, they would have had to have thought that the 'C' rune was an 'R' rune, but they had already deciphered the word 'coast', so they knew what the 'C' rune was. The 'O's are the same rune and the 'A's are the same rune, plus there is one rune for every letter, so it it's a direct letter-by-letter translation.
Plot hole: In the scene where Willie takes Skip to the army recruiter, the recruiter classifies Skip as 4-F because one of his testicles hasn't dropped. But seconds later when Skip stands on his rear feet, it is apparent that Willie, well let's just say that a pair beats an ace high.
Plot hole: At the end when the gang get home to Andy's room, it's night time and the luggage trolley they drove home in is outside the neighbour's house. The next morning it's still there. But we see an ad with the 'chicken man' looking very sad because he lost Woody and the others. How could he have gone to Tokyo, realised the dolls were missing, then zoomed back to Tri County to do the ad the next day? While saving Woody, the toys explicitly say that Andy is returning home the following morning. They must have made it in one night, or they would have missed Andy's return.
Plot hole: After Pikachu and Mewtwo begin falling down, Tim is suddenly on the ground in a matter of seconds, with little to no time to arrive there. There are multiple stairs, and he does not have any Pokémon to help him get down. He couldn't have gotten to the ground that fast.
Plot hole: We don't see any herbivores in the underground world - just fish and little birds. A T-Rex would need lots of big game to survive.
Plot hole: After Hannigan feels guilty for what she did, she confesses to the girls, and they find Mr. Stacks to tell him. The fact is, they went straight to where he worked - but Annie never told them the destination, and Guy himself never told Hannigan where it was either. So, how did they get there, and most importantly, know where it was?
Plot hole: When Erica crashes at the Huston Raceway Park a helicopter from the University of Utah lands to pick her up, it doesn't make much sense to fly a trauma patient over three states; At least not until she is immediately stabilized at a local hospital. We even see a truck from the Huston International Raceway drive up to the accident.