On the first day of my upper level quantum mechanics class, I discuss exactly the sort of systems that you've asked about here. Unfortunately, it turns out that "common sense" is not in fact an accurate guide to the behavior of our universe (especially on an atomic scale). This is deeply frustrating, but in the end, the universe doesn't care.

Specifically, I introduce the idea of a Stern-Gerlach experiment to measure the spin of an electron along specific directions. If you prepare an electron in (say) a "+z" state (which is absolutely unique and unambiguous) and then measure its spin along the perpendicular x-axis, the results are 50/50 (and completely unpredictable).

At this point, your intuition is crying out, "We must have just overlooked some distinguishing detail in that initial +z state!" But it turns out that there are experimentally testable predictions of that sort of "hidden information" theory that differ from the predictions of quantum theory (look up "Bell inequalities"), and experiments always come back saying that the quantum description is correct.