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 Christopher Plummer is hanging on the blown up bridge section, he is at the bottom rung. When Harrison comes to rescue him in the next shot Plummer is no longer at the last rung in the long shot. Then he is back at the last rung when Harrison reaches down to lift him up.
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.
Halloran, while on leave in London, wears his leather A-2 flight jacket. A-2 jackets were considered "flying clothes," would not have been worn off base, and certainly not while on leave in London. The proper uniform would have been a cloth "Class A" dress coat.
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.
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.
When Halloran first meets Margaret in London, he tells her he flies MiG 25s. The first prototype of this Russian fighter flew in 1964. If he was in London, based an hour and a half away, he was undoubtedly with the 8th Air Force, flying B17's.
When being chased from the farmhouse the two lead vehicles are a motor cycle with a side car and a kubelwagon. When they get near the big ditch the lead chaser is suddenly a single motorcycle. After the ditch jump the other chase vehicles don't show up right away. When they do the vehicle she now includes a tank. There was no tank earlier at the farm nor would the Germans have sent a tank to catch a couple of spies.
While Harrison and Lesley are in the cafe having tea, Lesley leaves her left glove on hiding her wedding ring. It would be odd if someone left one glove on. Then the glove is pulled off later, after the lengthy bomb raids where the two lovers have been huddled together for a while, to reveal the ring.
When Harrison and Christopher escape the SS building, the guards in the downstairs hall are not there when they exit although they were there seconds earlier when the four German soldiers entered the building and walked down the hall. The escape was simplified without the guards.
Christopher Plummer takes the place of Wells for the mission but when he parachutes and lands he has no sense of direction to find the town. He is totally reliant on Harrison Ford who is not supposed to be with him. Harrison's character can't speak French or German and has no training for espionage.
Strollers in a park usually walk in the same pattern as one-lane vehicle traffic travelling in opposite directions in that nation. When the two gentlemen stroll and talk in the "British" park, the opposing strollers are seen doing so in the American fashion.