Other mistake: In the scene where Ecks is chasing Sever, you see Ecks put a shell into an open chambered shotgun. This means that there is only one shell in the gun. A moment later when he yells stop inside the building he cocks the gun again. Thus, he is holding up Sever without any shells in the gun.
Factual error: Why are the FBI investigating and following their case if it's in Canada? The FBI or any other law enforcement agency in the US has no jurisdiction in Canada.
Factual error: After Ecks has just been buried by the metal pipes he shoots the guy who comes to kill him. He then uses his gun to help him up. I know someone who was in the army. Rule number 1. Never put your muzzle in the dirt. Then Ecks put his weight on the gun, forcing it deeper into the dirt. (01:11:00)