Shots of the train traveling through the countryside were stock footage, and were not specifically of the Flying Scotsman.
Every time the train with the robbers on board is seen steaming through the night, it features a different locomotive and coaches - often of different regions of British Railways. As the "Flying Scot" moves off, the words 'Paddington, Birmingham and Shrewsbury' are seen on the coach side. Hardly leaving from Scotland.
When Phil is trying to break into the adjoining compartment in the railway carriage, he drills a series of holes in a ring around the edge of the wooden panel. At one point, the drill bit breaks. In the next shot, after he has replaced the broken bit with a new one, there are fewer holes, showing that this is an earlier shot from before the one where the drill bit broke.
During the first journey, when the train arrives in London "overnight", it is still dark.
The Flying Scotsman train terminates at Kings Cross Station, not Paddington Station.
The same scene of Paddington Station is used at the beginning (where an announcement is made of a train going to London) and end of the film.
The robbers' electric drill would have worked well in Beaconsfield Studios' railway compartment mock-up, with access to mains electricity. Used in an actual railway carriage, the tool would have needed an AC/DC selector.
Whilst the 3 main characters are in their first class coach, Ronnie speaks of getting off "this locomotive". They are in a "carriage" or "coach". They are on a "train". They are most certainly not on a "locomotive".
On both occasions when the train is seen pulling out of the station a board on one of the carriages can be seen which reads Paddington Birmingham Shrewsbury. A completely different route to London to Glasgow.
Having ripped the upholstery apart, and removed a huge section of the dividing panel, at the end of the film the gang seem to have miraculously managed to put the carriage back together exactly as they found it.