Of course there is, we come across it all the time, in one of our products (CAD), somebody may have something selected in the diagram, there are modifier keys which apply temporary transforms while held down, it's possible the user selects some random toolbar option or menu option which given the complexity of the program fails to correctly apply the transform.

All operations were perfectly valid to "do", but only the combination of them cause the issue. As a program gets bigger and more complex it's easier to miss cases like this - the developer tests the standard UI cases but misses more obscure ones.