Posting this here incase this happens to anyone else and I dont know where else to put it. :
If you make a follower camp one z level above your autosort zones and they are on the same tile it might pull them up a level.
You can fix this through notepad++ instead of taking forever to do it manually.
Find your save location>world>open the zones.JSON file there(itll be preceded by a weird string of text) batch replace all of the y coords with whatever z level your base is on.
done.
(PLEASE BE ADVISED THIS WILL CHANGE ALL OF YOUR ZONES Z LEVELS.
If you only want to change some then youll have to find them in that fill by using the search function and replacing the y coord.