When the signalman steps out of the tunnel shortly after the accident inside (which result in a still burning fire at the time of the shot) the tunnel is issuing forth large amounts of smoke but there is no red glow one would expect if a fire was burning a short way down it.
When there is a close up of the bride lying lifeless near the track, then a wider shot, she's now lying right next to the railway sleepers and with her arms clearly positioned differently.
The bell codes used in the film, whilst generally accurate are sent in the wrong order. The signalman also holds down the plungers for too short a period of time, and only ever accepts trains, rather than passing them on.
The signalman uses a red flag to stop the train whereas it is clear that a home signal is provided.
Where the path is cut into the side of the cutting it is obvious it is of new make, not a well worn path used by the signalman every day. It can even be seen spilling onto the rails in one or two shots. This is because the signalbox is a fake, the nearest signalbox in reality is about two miles away.
The signalbox had no wire or point rodding runs emerging from the front of it.
Denholm Elliott's surname is misspelt as "ELLIOT" on the opening credits. It is spelled correctly on the closing credits.
In the first shot of the traveller down in the cutting, there are a number of concrete sleepers (or ties, the beams used to hold the rails together). These were invented well after 1900, and were not used regularly until the 1960s.
In one shot, a type of wire fence is seen that was not used until after WW2.
In one shot, on a beam holding up the shelf on which is the signalling equipment, there are three detonators (a form of explosive warning for railway drivers used in fog) painted yellow. They were not painted yellow until the 1960s.
The Locomotive used, 5764, is in fact of a design from the 1930s. However it is given the earlier livery, and is very similar to locomotives from 1900.
The hat of the Traveller is of a slightly earlier period than the rest of the costumes in the film. Whilst accurate for the time judging by his cravat and collar he is fairly well-to-do, and by 1900 the high bowler was more lower class wear.
At two points the Signal-Man writes in the logbook with his left hand. At the time his character would have been a child, the 1850s-60s, left handed children were forced to use their right hand. A left handed person would have been very rare indeed.