As it is rooms are limited to sharing a single door even if they are placed in such a way that their designs in rooms.xml would allow them to share more than one. If it is possible I feel this restriction should be reversed. This would make things a bit more interesting, and much more importantly Under the current system the rare occasions where two "#D#" areas butt up against each other without actually sharing a door it creates one of those glitches where the wall is too short and so wall traps and wall decorations display improperly as a result. (On a related note, two rooms aligned so that they can share a door should also share a door even if it would cause the dungeon's design to reconverge instead of just branching like it usually does)
Uh, they totally can. http://community.gaslampgames.com/threads/from-a-mod-im-working-on.3452/#post-38098
Are you sure that's not two interior rooms that you've cut a hole between with Digging Ray or the Mighty Auger?
I have tested this extensively whole modding. Rooms can share multiple doors, it just doesn't happen often barring specific circumstances or specifically shaped rooms.