Who pushed the box?

In our understanding of how nature works, there is an unspoken assumption that things are caused by some other things. For example, when we see someone pushing a box, we immediately assume that the force applied on the box is causing the motion of the box. The notion of causation is so ingrained that all action verbs contain an implicit assumption - I "pushed" the box means I caused the box to move. And yet, the laws of physics don't seem to deal with causation explicitly. Newton's second law merely says that force and acceleration are constrained to be proportional to each other, and not that the force causes acceleration.

After all, all we know from experiment is that force and acceleration go hand-in-hand. Where we see one, the other is always there. The idea that acceleration follows from force is a human belief. It might as well be that behind the scenes, someone is looking at the motion of all objects and causing a force to be applied to them. Then did we just arbitrarily choose force to be the cause and acceleration to be the effect? Or is it just too deeply programmed into our brains?

I think we label events as "cause" and "effect" based on the fact that a single "effect" might have multiple likely "causes" while a "cause" always has the same effect. For example, we observe, in separate events, that two massive balls accelerate towards each other and that two oppositely charged balls accelerate towards each other. Whenever we've observed two massive balls, they're always found to be accelerating closer, and so also when we've observed two charged balls. However, when we observe two balls accelerating towards each other, they're seen to be either oppositely charged or massive (or magnetic or whatever). It is by this asymmetry between force and acceleration that we label gravitational, electrical, and nuclear forces as "causes" the acceleration as the "effect". In logical terms, if an event implies another, the first is the cause, the second is the effect.

This is probably what makes quantum mechanics so counter-intuitive. What we classically considered as "causes" can now have multiple possible "effects". If we we throw an electron at a wall, sometimes the electron bounces back and sometimes it goes through. We got around the issue by saying that there is still causality - forces cause wavefunctions. That is, a force always causes the same wavefunction, whereas a wavefunction could have been generated by different possible forces. But that still leaves the question open - what caused the electron to bounce back some times and go through the rest of the time? Or perhaps, the notion of causality simply does not work in the quantum world.