The Volkswagen Kübelwagen in which the Oberst was driven to headquarters, had license plates marked WH or Wehrmacht Heer for ground forces. As an SS vehicle carrying an Oberst (Colonel), it would not have WH, but the distinctive runes of the SS.
When making the first bomb run in the B-25, and the right engine was hit and "feathered", the aircraft remained in formation at the same speed. Loss of an engine makes this an impossibility due to the loss of thrust.
In the French Gestapo Headquarters, SS personnel are addressing each other using German Army titles. The SS used separate ranks than the Army which would always be used when addressing other SS members.
USAF crews flew daylight missions over Europe. Halloran would not have had sufficient night-flying experience to carry out the mission with Sellinger. It is likely that a different type of plane would have been used as well, one less noticeable.
The headquarters in Lyon is lit up at night with bright lights shining through its large windows. It would have had blackout curtains with no light showing through. Similarly, in the pursuit through the streets, isolated shops are seen to have their front windows lit up.