Deliberate mistake: After Wolverine arrives at 3 Mile Island he approaches through a thick fog. Above him are a series of conveyor belts that are used at a coal power plant, not a nuclear plant such as 3 Mile Island. The belts are unique to coal mines and coal power plants, and would not be found at a nuclear power plant. The filmmakers obviously couldn't film on the site of a nuclear plant, so filmed on a coal plant to fill in.
Deliberate mistake: When Selfridge says "Pull the plug" after Hometree is destroyed, two soldiers, one male and one female, go to shut off Jake and Grace's avatar links. The female soldier goes straight to Grace's link and terminates it, but the male soldier gets delayed (punched by Norm) before he can terminate Jake's link. This is deliberately shown out of sequence - we see Jake's link terminated before Grace's. The result is that we see Grace's avatar fall unconscious when Jake's link is terminated, and Jake's avatar fall unconscious when Grace's link is terminated.
Deliberate mistake: After the SAD unit shoots down the command module, Christopher falls to his knees in sadness. In the next shot, the mercenary supposed to be pointing his gun at his head is looking and pointing as if Christopher was still standing, as revealed when he actually gets back up again.
Deliberate mistake: When Sam is watching the security footage of his predecessors being disintegrated in the chamber, the disintegration happens the instant the coffin door is shut. However when he goes in to test it himself there is a ~60 second wait as a congratulatory video plays before the disintegration occurs. (01:00:00)