I have noticed this in track circuit block, that the last tile in front of signal is somehow ignored. The signal in rear goes off and reservation is made even if this last tile is occupied. It is most noticeable with trains that are only one tile long. If they are held at a signal at danger, the next train is allowed to proceed into the block that should be still considered occupied by the 1-tile short train. See http://server.exp.simutrans.com/screenshots/simscr27.jpg
I have noticed that this happens only if directional (blue) reservations are involved.