In some shots of the departing deportation train, it can clearly be seen that the goods wagons used bear the inscription "UIC St" and a rather long wagon number. Both things belong to the international UIC numbering system, not introduced before 1965.
In the opening shot of the train crossing the viaduct, the coaches are BR Mk1 ones, which were not built until the 1950's yet the interior shots of the train show LNER on the antimacassar, which would be correct.
There are several train scenes but in most (not all) of them the sound effects, mainly the whistle, are those of North American trains. European steam engines had a very different sound. Even the sound of the tracks is different in Europe because of a different type of roadbed.
In the opening shot, a train carrying Charlotte to London is shown crossing a viaduct in the Scottish Highlands. The viaduct in question is the Glenfinnan viaduct, and in the distance you can see the Glenfinnan Monument to Bonny Prince Charlie. The train is clearly traveling North, away from London.
When the resistance near Lesignac are blowing up the ammunition train, the locomotive is clearly shown as a British Standard Class 2-10-0 Number 92240. This class of locomotive was not introduced until 1954 and Number 92240 was not built until 1958.
The German colors during the Nazi Regime were actually Black, White and Red. These were also the colors of the N.S.D.A.P. and were present on the shield of the German helmets of the Wehrmacht and all of the flags at this time. So the Bundesrepublik Deutschland colors of Black, Red and Yellow are not appropriate for the film.
Most, if not all, of the scenes in Vichy France are shown during the dormant season, i.e., winter/early spring when the trees are bare leaved.
However, when the story jumps forward ("6 months later") to a scene in bomb damaged London, we can see a bare leaved tree in the background when (6 months afterwards) it should have been in its summer foliage.
At the beginning of the film Charlotte talks to Peter about the approach to go to France. In reality prospective SOE Agents would have been sworn to secrecy on the approach let alone talk about what it was about.
The goof item below may give away important plot points.
When Charlotte types the letter near the end of the film, she regularly uses the shift key while typing, so the letter is in proper sentence case. When Levade reads it, from behind the letter is clearly all in upper case, but a second later when you see the letter from the front it is in proper sentence case again.