Playing the game I notice the buses do not occupy the hole space in the bus stops, at least the smaller ones (including the old twin coach), so why can't a second bus stop just behind it? If there's some room in the bus stop, why the second bus keeps wayting in the previous square instead of stopping along?
Simutrans is tile based, so vehicles either occupy a tile or they don't. Making this more fine grained is both a lot of work, but might also cause performance problems on well developed maps.