This maybe working as intended, but there seems to be an issue with one particular type of room. This is the room that has a set of stairs going down under double stone slab archway. The room has 6 possible exits, however, the ones that are to the left when facing to the archway seem to be blocked off by walls, while it is actually connected. See screenshots, one instance of lower left connection being walled off, and another with upper left (Sorry I've mined the archway in this one). Both are perfect connections to the other room/corridor. In both cases, the sections behind te walls could not be accessed through any other path within the stronghold.
This can be observed with seed 818010429. There is a village at/near the spawn point (actually I think these are two overlapping villages). There are two wells in the village. The stronghold is 4-5 blocks down from the bottom of one of the wells. The first instance is found in the first archway encounter after climbing down the stairs to which the hole in the well leads.