When a terminus station is the same length as the convoy stopping at it (x tiles), the train will tend to reserve space incorrectly; it will often not reserve the last tile, leaving the convoy hanging out, resulting in a convoy too long for the stop message.
Can you upload a saved game in which this can reliably be reproduced?
http://www.mediafire.com/download/7v9edqndsdd43vq/tass15.sve
Affects Whippoorwill and the end station on the other end.
Hmm - I have seen some convoys not routing to the last tile, but this seems to cease after a while, and does not appear to affect the long convoys (the expresses hauled by the GNR C2 class). Can you mention a specific service to which this happens?