The "Tirano Tunnel" between Italy and Switzerland depicted in the film does not exist. Although Tirano is a real place, and there is indeed a railway line leading over the route shown on the plotting map (through the Albula Pass), the line is a narrow-gauge one and the train depicted would not have been able to use it.
During one of the scenes depicting 'Eurorail Control (train control center) - Munich, Germany', a British Rail Class 101 DMU showing 'Network Southeast' livery is shown passing through the shot.
Network Southeast and the Class 101 DMU were a train company and train that only operated within the United Kingdom. They never operated in Germany.
Malcolm asks Sabrina if she is familiar with the M203 grenade launcher. Later you see her with a shoulder fired grenade launcher. In reality, the M203 is much smaller, and it mounts under the barrel of an M-16A2 5.56mm assault rife.
There is no such thing as a central dispatch for all European railway. If there were, it would have had to be manned by a couple of thousand dispatchers in order to control all points, signals, trains, shunting operations and track works. In the movie only two different dispatchers are portrayed and not many more, if any, are visible.
Most of the German, Swiss and Italian railways operate under electric power supplied through overhead catenary. This includes all the major lines such as those connecting Bremen with Stuttgart which are also at least double track. All the lines in the movie are single track and lack catenary which clearly indicates them being branch lines.
With the locomotive depicted in the movie it will be impossible to pass from the cars into the locomotive without going on the external side of the locomotive because the locomotive is one cabin type. There is also an engines room view when the characters pass from cars into the locomotive witch is also inaccurate because this type of locomotive does not have actually an engines room, all the engine and aggregates are accessible through several doors from the exterior of the locomotive
The "terrorist" helicopter, attacking the train, is actually a Slovenian police chopper Bell-212, in regular police paint scheme and with regular police markings (at the time the movie was filmed) clearly visible.
At 1:06:00 into the film, Tierney is talking to Philpot on a Motorola 8000 series cellular phone. The battery pack has not been fully inserted into the back of the phone, which would therefore not be capable of making or receiving any calls.