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.
Factual error: When the action moves to England after the failed award ceremony, the British Union Flag hanging from the wall is upside down. The broad white band should be at the top left (nearest the top of the flag pole).
Continuity mistake: In the scene where Tulio visits Linda in Minnesota, there are two blue pens or pencils on the table. When Tulio throws Blu, the two pens or pencils have disappeared.
Continuity mistake: Tony Trihull appears when Finn McMissile begins chasing Professor Z. It also shows when Tony uses his magnet. When it is used, Finn's equipment are pulled by the magnet, which includes his bullets. Those bullets are black when all of them were going out. However, when they are pulled onto the magnet they are grey.Paul Thomas Backes
Continuity mistake: When Puss is telling his childhood story and he is in the orphanage, when Boy Blue spins Humpty, Humpty's hat is off, it comes back later in another shot.
Factual error: In the scene straight after the opening credits we are taken to Baker Street where construction work is being done. This work is identified by a sign with a logo as being for the underground line. The logo type face was developed by a Mr. Edward Johnston for London Underground from 1913 but the distinctive typeface used in the film was not in place until 1919. This is obviously long after the 1891 setting of the film.
Continuity mistake: There is a scene where Hugo is on the station and sees a key down on the tracks. There are two seperate shots of the key and both times it is buried in the stones next to a sleeper. Then Hugo jumps down onto the tracks to pick it up and its now quite sat on the middle of the sleeper when he picks it up. (01:22:30 - 01:23:10)
Factual error: When Cattleya escapes through the sewer drain and winds up in front of the U.S. Embassy, she uncovers the manhole all by herself. Impossible for such a young child to do.
Continuity mistake: When Tick Tock freezes Rebecca and Cecil, they are in one position, and when they go to the close up of them frozen, they are in a different position. When it zooms back out again they are in the first position. Also, when they are frozen moving on the conveyor belt, they are back in the position they were in on the close up shot. (00:47:50 - 00:48:10)