Do the following:
Build things like displayed in (1) with the bus travelling between stops 2 and 3.
Build a ship and add a line with a halt in front of stop 3 an one on the tile displayed in (2).
Now the connections are displayed in (3).
Build a new bus stop like shown in (4).
Now, the ship changed it's schedule and stopping at halt 2 (6).
But now the connections of the stops are wrong: (7).
This bug is caused by planquadrat_t::add_to_haltlist(), since this routine may alter the order of halts in planquadrat_t::haltlist, ships already stop at the first halt of this list and the change is not correctly reported to the "routing system".
If it's the intended behaviour, that ships can halt near bus stops and that the stop of a ship can change, if a new stop is created, then I will have a look on this bug, when I reorganise the routing of goods (http://forum.simutrans.com/index.php?topic=1016.0 (http://forum.simutrans.com/index.php?topic=1016.0)).
Well it is partly indend; The only thing to ease that would be looking if the stop in question has a dock. Others than that it does not make sense to build so many overlapping stations.
I would file it under know bug. Imho the effort of fixing that compared to the time this error occurs (was reported once a nice feature in the old old forum) is not worth the effort.