The example of the OP seems to be the "opposite" of a blessing in disguise in the sense that a setback had disastrous as opposed to beneficial consequences. We might call such a setback a disaster in the making:
in the process of happening
It became clear that this was a disaster in the making and we had no way of coping with it.
Cambridge Dictionary of American Idioms Copyright © Cambridge University Press 2003.
No one could have known it in advance, but in retrospect, that setback in car service was a disaster in the making for John Forbes Nash, Jr.