[A]tomic nuclei are pretty hard to peer into. But that’s not the root of the problem. It’s that we simply can’t, for quantum processes, talk about a historical progression of events that led to a given outcome. There’s no story of how it ‘got’ to be that way.
Everything that seems strange about quantum mechanics comes down to measurement. If we take a look, the quantum system behaves one way. If we don’t, the system does something else. What’s more, different ways of looking can elicit apparently mutually contradictory answers. If we look at a system one way, we see this; but if we look at the same system another way, we see not merely that but not this. The object went through one slit; no, it went through both. How can that be? How can ‘the way nature behaves’ depend on how – or if – we choose to observe it?
Wavefunction collapse is a generator of knowledge: it is not so much a process that gives us the answers, but is the process by which answers are created. The outcome of that process can’t, in general, be predicted with certainty, but quantum mechanics gives us a method for calculating the probabilities of particular outcomes. That’s all we can ask for.