Continuity mistake: When Steadman is watching the agent put the bags that contain the remains of Veronica Donovan into the trunk of the silver car, the license plate changes between shots. The first time we see the car, the plate reads "1029Q", the second time (close-up shot as the agent closes the trunk) it reads "9417X".
Continuity mistake: When Lincoln and Michael are talking on the little pier, Michael talks about Westmoreland and his relationship to the truth. Lincoln has his head turned towards Michael through this, but as Michael says "There'd be no reason for him to lie about it", the angle changes and Lincoln is suddenly staring straight ahead, with no time to turn his head between shots.
Continuity mistake: When Steadman takes out his gun, he presses it to the back of Veronica's head. She does not flinch or shy away from the gun, but in the next shot, a close-up of Steadman, the gun muzzle is pointed at the camera with Veronica off-screen, and so the gun is suddenly not touching her.
Continuity mistake: When Mahone is in Scofield's apartment the show flashes back to an overhead view of Scofield planning on the wall while Mahone is tracing over the holes in the wall from where Scofield was tacking papers up. The mistake is in the flooring, the laminate flooring is a much lighter flooring than when Scofield was there two months prior.