Plot hole: At the end of the film the boss says that he and Miss Fitzgerald are going to go on holiday together to Paris (talking about the actual city, not the secret code they have invented). However, the film is set in 1940 and Paris would have been an unusual place to take a holiday at this time, considering France was in the middle of a war... Pretty dangerous for civilians even though America was still neutral at the time.
Plot hole: When the police search the white car and the barn they fail to find the compartment in the car behind the boot in which the decoding equipment was hidden. This is completely improbable. It was a standard car, the compartment was not a secret add on, and the police were supposed to undertake a thorough search of everything.
Plot hole: In the middle of the film, after the custody hearing, Frank shows up at an event. Danny pretends that Frank dropped his wallet in order to have a brief conversation with his dad. Later, Rick confronts him about what they talked about. What does Rick expect? It's not like Danny will never be allowed to visit his father again. They are going to talk at some point. For Vince to expect that he will never talk to his father again is unrealistic.
Plot hole: When Margaret has to collect the $50,000, she goes around to various banks trying to get a loan on their house, which she can't get because her husband, co-owner of the house, isn't around. Why couldn't she just have taken the papers, said she was going to take them home to her husband, forged his signature, and brought them back? You can't exactly say she has either moral problems or isn't devious enough, since we've already seen her stuff a body into a dinghy, toss it into the lake, and come back to her house looking fairly normal.
Plot hole: When Grace Stewart sends Ann out of the music room for "lying," the hall is visible as she opens the door - with lots of light from windows bursting in. I know it turns out not to matter, but the child would have screamed.
Plot hole: Summer vacation couldn't be taken away just because it is winter, (or just snowy), they could just go by the date.
Plot hole: The kids in Soneji's class use an encrypted GIF algorithm to pass notes to each other and that "drives the teachers crazy", since they are unable to catch cheaters that way. But how do they do that? Easy, they have a message system in place installed on their workstations, that warns them with a big pop-up that they've got "A new message"! It would be easy to sanction and prevent the cheating by simply removing the chat application, no matter if they use it to chat directly or pass Michael Jordan photos as shown in the movie, which they have no business doing during an assignment anyway.
Plot hole: When the "Blue Bird" patient finally sees the Blue Jay, he starts excitedly shouting "Blue Bird! Blue Bird!" This uprising causes a riot in the institution, and in the immediate exterior shot of the building, everyone from all four floors already know and are staring out the window at the bird. Within the time-frame of the scene only the people on the floor which saw the bird would actually know about this. Psych ward floors are kept separated as it is even noted by an attendant when he said, "Do you want to go to the fourth floor?" which indicates that the floors are kept separate. This was deliberately done for dramatic purposes. (00:44:00 - 00:45:00)
Plot hole: Early in the film, we learn that the former prostitute Annie Crook is married to and has an infant daughter (Alice) with Prince Edward Albert Victor. Secretly outraged, Queen Victoria dispatches various high-ranking operatives to eliminate this potential royal scandal. To that end, Prince Edward Albert Victor is secreted away, and his wife Annie Crook is kidnapped and barbarically lobotomized. We then learn that he baby, Alice (who was fortunately in the care of two other prostitutes at the time of the kidnapping), was sent to live with the parents of Annie Crook, no doubt saving the baby's life. That is the last time we hear of baby Alice until near the end of the film, where we are puzzled to learn that Alice was not sent to live with her grandparents at all, as stated earlier. Rather, the prostitute Mary Kelly took baby Alice away from an orphanage to raise as her own. No explanation is offered for this discrepancy.
Plot hole: The female employee says he's going to inherit everything, he gets it all. No he only gets 51%, the 7 dwarfs still make many decisions. (00:10:37)