Sorry to hijack this thread, but it's one of the few places I've found people actively discussing this issue, which has plagued me over several different saves and mod lists.
I've noticed that this happens frequently, though I don't think exclusively, when I enter interior locations. In one recent save I'm inside Vault 81, but looking at my save in Fallrim Tools, I see active workshop scripts that say they're trying to assign a settler to something ("workshopparentscript.TryToAsignResourceObjectsPUBLIC()"). Obviously that's not my doing, I'm not even in the overworld. Could this be Sim Settlements attempting to assign a new recruit to a plot somewhere?
Another script I see running is "workshopnpcscript.::remote_FollowersScript_CompanionChange()," and a while back (over an hour ago in real time) I swapped from Ada to Piper. They're sort of co-leading Sunshine Co-Op, depending on who I need at the moment, and I use RotC's pop-up option to reassign the other as leader each time. I had this issue before RotC/3.0 released, so I doubt it's related, but...
In this save I only have 7 active scripts. I'm at a loss here because, due to having to constantly roll back saves, I have to keep redoing about 50% of my quests/dungeon dives to maintain the ability to assign settlers, and that's just not fun. I lost my first save because of this bug as well, and I started a fresh playthrough to try to avoid it, but it keeps popping up. I'm paranoid and constantly check to make sure I can reassign settlers (then, when successful, I load the previous save as to not create more script lag by assigning and unassigning settlers), so before I set off on an adventure, I know I have the ability to assign. Then I get back, dump loot, craft, sell things, and remember to check a settler, only to find I can no longer assign. It's pretty heartbreaking.
Not sure if it's worth it, but in case it's helpful, I uploaded a few recent saves to Dropbox. 94 is the most recent save I can find where I can assign settlers, 96 is the save when I'm inside Vault 81 (and I did load that one and leave immediately to try and assign a settler, but it didn't work, so I know by this point the bug is present), and 98 is my last/most current save. Dropbox link:
https://www.dropbox.com/sh/xmp4nja8mv0eirx/AADGSLaUGtcs1rvCbMXCPfzra?dl=0