This happened to me in both Wailon Lodge and Passwater Cove. Only with the "minimalist partition", none of the others. I haven't tried using it on the other maps yet.
Workaround I found is to delete the square that the piece of the wall is left standing on, and then build whatever you need to build. When you're done, replace the square you deleted. You may need to move or delete a room to do so. If you have to delete a room, make sure you have it saved as a template first so you don't have to rebuild from scratch! It's annoying if you're editing your building a lot, but it works.
On the Passwater Cove museum map, I encountered an unremovable partition wall floating on a corner of the building era. The partition wall can not be removed either by editing the building or using the wall removal tool. The partition wall is also flagged as an invalid object, preventing any edits to the building. I encountered this bug during the campaign mode and am now unable to continue playing, since I can no longer expand the museum.