I finally found what mod caused the problem (well, I think :p)

Place something with "multiple entities" (like capsule in SE, nixie tube, or an attach-note)
Then, in map editor, undo it.
With instant deconstruction checked or not, it will instantly be removed. And the "sub entities" will remain (normally removed with the "main" entity)

Do you change something with undo or (instant) deconstruction that can cause this ?

In order for this mod to function at all, I had to nuke the vanilla undo and replace it with my own.
As it turns out, that's really easy to do when it's the exact opposite of redo, I literally just have a thing that inverts the input.
I think it's really easy to fix, when I initially made the mod I forgot to raise script destroy events whenever I delete something.

Just released 0.2.9 which should fix it.