There are no bullet holes seen in the floor after Hogan, as a Wehrmacht officer, fires his machine gun into the floor towards the Gestapo soldiers.
At the end, when General von Kattenhorn drives away, there is a nice set of tire tracks from Colonel Feldkamp's car. When Hogan gets up minutes later (after both cars blow up) the tire tracks are gone.
Hogan enters the office and tells Hilda to stand in front of the window and cross her fingers. From the outside there is no window. This is where the bulletin board is on the exterior of the office.
When Hogan's men have the Gestapo soldiers against a wall in a basement, Hogan fires his machine gun at the floor, blowing a line of holes in it. The shreds around the holes reveal a wooden floor, very unusual in an unfinished basement, where the floors would have been stone, dirt or concrete.
In the introduction, Newkirk drives into Stalag 13 in Schnitzer's truck, gets out of the truck, throws his disguise overcoat and hat into the truck, and gets his uniform clothing back in place, just before Schultz arrives. The problem is that Schnitzer is nowhere to be found, so, after Greta and LeBeau get out of the truck, there is no one to drive the car away. Schnitzer's truck sitting in the middle of the compound, with no Schnitzer to drive it away, would cause many questions.