The train is described as a munitions train with one passenger car at the end, yet as the train passes it is clear that all the cars are passenger cars.
Hogan plants the bomb in the last car, yet when the train explodes, the first explosion happens in one of the front cars.
When the gang sets up to stop the train, they wait until the train is almost there before changing the signal. Trains do not stop instantly, so they really would have had to change the signal much earlier to get the train to stop at the point they wanted it to stop.
Carter, as Hauptmann Carterheim, has a big mole on his right cheek. This is a giveaway that he may be an impostor.
Update: The mole only a giveaway if the people he is talking to know him as Carter. The Gestapo that he is talking to don't know him at all.
Update: The mole only a giveaway if the people he is talking to know him as Carter. The Gestapo that he is talking to don't know him at all.
At one point, there is a scene of the train engine. The numbers on the engine are backwards indicating that the film was flipped.
At one point, Newkirk's Nazi insignia is reversed.
During the 3:00 special formation, the shadows change from being very long (probably near sunset) to almost non-existent (probably early afternoon) during the formation and the associated diversion, indicating that the whole scene was filmed out of order. Compare the lengths of the shadows cast by Klink and Schultz just before and just after the truck comes in with the shadow cast by the truck. Also, when Schultz goes running from the truck back to the diversion, his shadow is much shorter than it was when he was standing beside Klink (before he went to help with the dogs). Also, when he goes running back, it is much brighter than when the formation began, so it was obviously earlier in the day. It is possible that the segments with the long shadows were shot in the early morning, and the other segments (with the shorter shadows) were shot later in the morning, but the result is the same - the shadows do not match up over the course of the scene.
Carter mentions the Pentagon regarding a message. Carter was imprisoned at Stalag 13 in 1942, and the Pentagon didn't finish construction until 1943.
There were reflections of production lights in the glasses of Gestapo men.