I have discovered that if I try to restart a saved session on some of the services on the London Commuter route, it disrupts the AI trains. This has happened to me on one of the Class 66 timetable routes and two of the scenario routes. What happens is that, shortly after I restart my service, one of the AI trains, just ahead of my train, does not restart after stopping for some reason. I am then stuck at a red signal, which never changes. Exactly where this happens will depend on where I restarted from, but it is repeatable. I have tried restarting the game, and even restarting the computer, but the fault recurs in the same place, relative to the starting point. However, if I play the scenario without interruption, I have no problems with the AI trains, and I reach my destination in good time.
Unfortunately, this is a somewhat common occurrence with saved games throughout TSW2. You might get lucky on occasion and things might work as they should when coming back to it, but it’s rare. Saves almost always mess up the sequencing with AI trains. I know it’s probably not the answer you’re hoping for, but the standard advice is to avoid saving and try to play through a service in one sitting. Sorry I can’t be of more help.
The saved game is basically broken, odds are about even at best it will restore properly. BML seems particularly bad, presumably because of the hugely complex timetable and multiple AI movements.
Are these stuck while at stations by any chance? I've had a similar issue where AI trains get stuck after a saved game.