Off the top of my head:

• Lightning (how does it happen?)

• Sleep; dreams (why do they exist?)

• Glass (thermodynamics of formation)

• Turbulence (when does it start?)

• Morphogenesis (how does a creature know what should go where?)

• Rain (it seems to start faster than models would predict)

• Ice (dynamics of slipperiness)

• Static electricity (which material will donate electrons?)

• General anaesthetic. (And the mechanism of a lot of drugs, e.g. paracetamol.)

That is from Patrick Collison.  It is a further interesting question how many of those questions will be answered by what is sometimes called AGI.  Perhaps none of them?  In at least some of those cases, what is scarce is experimental data, not reasoning per se.