I am still trying to figure this out, but it's happened 4-5 times now and I'm about to punch my monitor.
Found this closed bug that sounds just like it:
I'm mainly using shift-alt while scaling up a sprite in very small amounts, larger than it's original size. (alt is a photoshop habit, I know it's not needed.)
However I don't remember it happening to me before r114.
(but I haven't been tweaking sprites this much either.)
none of my attempts to recreate cause it to happen. I would say it's rare enough you forget to be careful before it happens again.