I found that in the aqueducts area, mobs tend to spawn on the sewage tiles, making them only hittable with magic. This is annoying for players running a melee build, and often leads to a softlock issue.
There is also an issue with spawning the secret room. If the path to the secret room happens to spawn on the side of a room that leads to another room, the secret room does not spawn. This has cheated me out of a path through the aqueduct, forcing me to take the regular path.
Lastly, knockback items are capable of pushing bosses out of bounds. It also leads to a softlock.