It's ridiculously easy to get this sort of thing to happen when doing patches. ESMify an ESP, load the CS, make some edits, and you'll end up with plenty of crud in places you weren't even looking at. Dialogue, landscape records, path grid records, cell records, you name it. The larger and more spread out the parent mod, the more likely you are to see it
Thanks for the directions - I'll see if I can reproduce it.
EDIT: Are the edits usually accompanied by "Failed to CreateGroupData for CELL form ..." errors ?
You might be able to cause some dirty edits by dropping a new item into the CS, then dragging it around in the render window making sure to cross as many cell boundaries as possible. Stop in each new one, then grab it and keep dragging. I think as the object leaves the previous cell, the data saying that cell is modified isn't properly cleared.
Another possibility, drop something in a cell, then delete it. Do the same in other cells.
I think that's how the CS works. It doesn't track references individually. When you move a ref into a cell and drop it there, the object list of the cell gets updated. Such an update flags the cell object/record as active. The same goes for dropping something and deleting it. As far it's concerned, you manipulated the cell's data in one way or another and that merits an 'active' flag.
I think some as yet unnamed hero is looking at the CSE.

Ah, there it is again! The sneaky 'CSE'. You folks seem to know something I don't ...