Plot hole: Where do the flyers come from that are in the bags that are carried out of the vault and into the van? Danny and Linus couldn't have taken them down there and there is no room with the Chinese man. They are carried out to the van before the SWAT team appears, which means they'd have to have been in the vault to start with? In the commentary by Steven Soderbergh he acknowledges that there's no explanation. (01:35:05)
Plot hole: How could the police miss finding Cybil in the trunk of Michael Zane's car when it was in an impound lot? They would have definitely searched the car if he was found in violation of a federal offence (for carrying the weapons). Even if they didn't do a search, they would certainly have heard the sounds that Cybil would have made from being locked in the trunk.
Plot hole: When the security guards enter the cage housing the blown safe there are no traces of the water used to break the safe - not even on the (dry) floor. This happens only minutes after the explosion sent the safe door and gallons of water across the cage.
Plot hole: How is it that the main character was able to follow her father's dead body to the coroner's office to see him put into a specific casket? She was a nine year old girl...no one noticed a little girl hanging around a morgue?
Suggested correction: Maybe the morgue workers didn't have the heart to eject a lone orphan from seeing her Dad for the last time?
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: 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 they are investigating the small box that was pulled out of the trunk of the car, the one with the doll, shouldn't they be wearing more protection? They are only wearing protection for their legs.
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: At the end, Pops is cleared of all charges. But the only thing he did was prove Leo lied about some things Pops supposedly did. Its highly unlikely the FBI would drop all the other charges that Pops had really done (illegal gambling, money laundering, etc).
Plot hole: When Marty, Ali and the hitman go back to the crime scene, they go over to the water where they threw Bobby's body. Marty throws up, leaving his DNA at the crime scene. And since he was Bobby's best friend, he's the number one suspect.
Suggested correction: Vomit doesn't contain DNA, unless said vomit contains blood.
Untrue. "While not all these bodily substances provide ideal DNA samples, testable DNA can often be extracted from all of them. In every case, what is being tested is the DNA contained in cells of human tissue, whether found on their own or carried by another substance, like earwax, sweat or mucus. Shed cells are also found in urine and feces, vomit, and even tears." https://www.nytimes.com/2010/11/02/science/02qna.html. Also https://www.mirror.co.uk/news/uk-news/violent-thug-caught-dna-vomit-4017184 "A violent thug who glassed a man in the face has been jailed after being traced down by DNA in his vomit."
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.