During the motorcycle chase scene they start off on a Harley Davidson Fat Boy. It changes to a Panhead springer, then back to a fat boy and finally at the junk yard a pan-head springer again.
During the motorcycle chase scene, a couple of clips are flipped: evidence for this is the exhaust pipes on the left hand side of the bike and Grace's bag hanging from her left shoulder instead of her right.
During the junkyard scene, at about the 57:40 mark , an agent hears something and turns and the camera view shows a junked car missing the front right door. As the agent starts running towards camera, the door reappears with the window intact. The Stranger kicks the door open to trip the agent, who falls over the top of it destroying the window and window-frame. When The Stranger steps out of the car and kicks the agent, the window and window-frame are intact once again.
The motorcycle in The Stranger was never a FatBoy. It is a stripped down Road King with the bags removed and the light nacelles painted to match. It does become a Springer in the junkyard but who would dare thrash on a collector when there's millions of Twin cams to beat on.
At the 45 minute mark when The Stranger steps out of the shower, and before he picks up the towel, he's already completely dry.