Other mistake: When Tris, Tobias and Caleb flee from Eric and troops they escape by running across train tracks, placing an oncoming train between themselves and the shooting troops. However in a shot of the group preparing to board the train, bullets can be seen impacting the side of the carriages all around them...but the firing troops are on the other side of the train.
Continuity mistake: Tris overpowers Peter in the testing chamber. After Jeanine says that she has enough guards, Tris pushes him away and turns around. A second later Peter is in the control room with Jeanine, his face already cleaned and without blood.