I feel your pain. Sometimes doors are rendered impassable because of slight changes in elevation. This occurs quite a lot in Final Blitzkrieg, as has been pointed out in other threads..
Also, some of the buildings introduced in Market-Garden had a problem with troops entering through the side of the building rather than the front or back door, this was then ported over to Final Blitzkrieg. As you mentioned it is a particular problem on the Aachen map as rather than being detached houses, they have been set into rows alongside the new FB building types, and therefore, the player has no idea which door the troops will end up being able to use.
Sadly, I don't think that the problem can be fixed using the current engine, unless scenario designers want to re-visit their work and remove the problematical buildings and post a new version of their campaigns or battles for us to destroy.