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.
Other mistake: When Ecks, his wife, and Sever are driving to Severs lair you can see that the cut on Ecks' cheek is just a sticker because there is a different reflection on his skin from the sunset.
Other mistake: Near the end in the train yard when everything was blown up there was a passenger train car still in tact with its windows still in it. The train car next to it was levelled.