Plot hole: One of Snape's memories show Lily telling baby Harry to be safe, be strong. That had to have occurred before Voldemort killed Lily. Snape was not in the house until after Lily was killed and Voldemort was gone. Only Lily and Harry should have had that memory, but not Snape.
Plot hole: Harry never notices that the name "Peter Pettigrew" appears on the Marauder's Map, right next to "Ronald Weasley." Way beyond a character mistake, as there's no way that wouldn't be cause for interest. If nothing else, Ron's brothers who had the map for years before giving it to Harry, would most certainly have wondered why their brother was sleeping with a person named Peter Pettigrew.
Plot hole: At the beginning of the movie, Hedwig rattles her cage, and Harry says apologetically, "I can't let you out, Hedwig; I'm not allowed to use magic outside of school." But he wouldn't have to use magic to let her out - the key is visible sticking out of the lock on the cage, so all he would have to do is turn the key. (00:01:10)
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.
Suggested correction: JK Rowling explained why Ron's brothers didn't wonder why Ron was sleeping with a man named Peter Pettigrew. Here is the link: https://scifi.stackexchange.com/questions/11447/why-couldnt-harry-or-anybody-else-see-peter-pettigrew-aka-scabbers-on-the-marau.
jon snow