It sounds like rails are broken somewhere, or if it is electric, some rails are not electrified. If it is neither of those, then somehow one of the stops on the line is not able to be reached, either because it no longer exists (deleted and replaced, but not close enough to take the spot), or because it is attached to a different rail altogether.
If none of these is true, then it is beyond my scope of understanding!
Edit : Maybe you told the train to stop? If you click on one and look in it’s main information window, just below the view of the train is start/stop and reverse buttons.
