More information,
including a work-around for those who need one.
First, it happens to be that it is precisely over an area where a trade depot used to be. Not all 25 squares, but at least 6 of the 9 middle squares, but definitely not all 9 of them; at least one of those was fine.
Second, floors, stairs, bridges, and so forth can be built on these squares, but not wall, fortifications, et cetera, that block movement. This is probably obvious, though. And building a door there makes the door built in a stuck-open state.
Third, building a raising bridge over the area, and then raising/lowering it destroys the phantom creature, allowing walls to be built where they couldn't be previously.
Fourth, I was reminded (because it happened again while testing all this) that I once had a problem with auto-save backups with this fortress. The game got stuck during a save on a season switch. I just killed the program through the task manager. The region1 folder and the region1-aut-1051 were not identical. The -aut-1051 folder was missing the unit-3910.dat file, and the region1 folder's world.sav file was around 8K smaller than the region1-aut-1051 folder's. I tried loading from the region1 folder, and all went well, so I didn't think much about it (just a sigh of relief). I did save a copy of these two folders, though, in case it became relevant (and just confirmed that the backup, although slightly different, loads fine as well). Let me know if they'd maybe be useful, and I can upload them somewhere. They are before I destroyed the trade depot though, so it's before I found the phantom-creature-in-the-way bug. I have separate saves for that.