If you press Shift+Arrow key to shift a selection, and then paint with the brush tool, hovering over the same pixels with the mouse causes them to disappear, often reappearing in a different location if you hover outside the area. The direction and amount you shift the selection affects the severity of the distance between what you thought you drew and what was actually drawn. More bizarrely, the effect sticks to each individual frame of the project and persists when you reopen it.
Update: It seems this is a side effect of this function not being disabled for the Background layer.