Good answer by Mojave. There is also a slight nuance of "trying", or even "trying to come to terms with"- if you don't understand calculus, then you just don't understand. However, if your brother suddenly moved, you couldn't get your head around it - you tried to understand his reasoning but you couldn't. Be sure to note that we almost never say "I got my head around it", it is almost always negative.

To take it one step further, the idea is if you could get your head around it, it would be inside your mind. You would understand it. But you just can't get your head around it. You can't understand it.

It means that they couldn't understand it. They couldn't understand why he moved. "Getting heads around" equates to using their brains together to try to figure something out.