This happens a lot to me when modifying any objects. Deleting sliders, slider points, moving slider points, deleting hitcircles. Sometimes I accidentally drag a slider longer than it was and suddenly it can't be undone! It doesn't seem to happen consistently either, so I have no clue what causes it or not. Ctrl+Z has basically been useless to me for several months now because of it
Edit: Forgot to mention, sometimes it doesn't properly undo selecting a group of objects. So if you move one, then select it among a group of several objects, then decide you want to undo moving the first object, it does not undo the selection, and moves all the objects that were selected after the undone move had been made- resulting in them being somewhere I had never put them.