Continuity mistake: When the Apes are trying to break into the mutant's church, Mendez looks towards the Alpha/Omega bomb, and is wearing a cream-colored jumpsuit with a purple sash. When the Apes do break in, his sash has disappeared. (01:25:50)
Continuity mistake: When the investigator begins confessing to the other police officers, one of them has him eat a handful of salt. After eating the salt, tiny salt grains can be seen on his lip, and can be seen on his lip for the following minute whilst he is trying to convince them he was the killer. When he says "But I left fingerprints all over her apartment", a larger amount of salt can be seen on his upper chin that wasn't there a minute earlier. (01:45:52 - 01:46:57)
Visible crew/equipment: When Mike and Susan prepare to start putting pieces of snow in the kettle, in the shot where Susan hands Mike the kettle, and he begins taking the lid off, the camera crew can be seen reflected on the kettle. (01:16:00)
Continuity mistake: During Prince Rupert's first appearance, he greets his uncle King Charles I by doffing his hat and putting it back on. In the close-up shot he is holding his hat in place but in the wide shot his hand is on his side.
Deliberate mistake: When the family first entry Three Chimneys they have a single lamp as a light source. Entering from the door at the rear of the shot, everything in front of them should be in darkness to the viewer, but it's lit. Things in the background are lit even though there would be no line of sight to the light source. This is because lighting was added on set to allow the viewer to see things better, even though it ruined the realism.