I have this problem too but on Cryptic made maps. Klingon Interior #2 and Arctic Mountains.
I didn't have these problems before. The mission is not published so this happens when playtesting it. Which makes the playtest impossible to do. Project ID ST-HHZUDQU9B
I've tried duplicating the Klingon Interior map and deleting it and picking it again. The BOffs fall through and end up at aprox 300 meters below me. Then they die. When on the Arctic Mountains map then I reset the map they were still dead. So I revived them and they fell through the floor right then and there, before my eyes. In a spot they didn't fall through before.
Hmm.. this makes me wonder.... would it be possible to have the maps use some sort of default pathing until published? Obviously this would still have limitations, but different, probably less severe limitations.