I think I found at least one cause of the AI trains to getting stuck! I was running the 6:53 AM a M3A local express last night and got stick at Crestwood on Track 2. So I moved to the lead train that got stuck which was a M7 also on Track 2 and took it over it had a green signal, but the train wouldn't move. Looked at the timetable for that train and it was suppose to be a local running on track 4 next stop would be Tuckahoe. I think the problem are the intermediate signals that lets the train bypass it crossing a switch it was suppose to take so now it get's confused when it's coming to a station it suppose to stop at but is on the wrong track.
