I think its all about exerperience and getting a feel.
Most of the time you can feel the horse start to tense up underneath you. And a thing I noticed with alot of riders is when this happens they do tense up and start to pull back. If you ride forward, then you give them little time to think about whats happening and more about what you are instructing to do. Sit deep, ride forward and give a good hard 'get up' if you have to.
I still get caught of by spooks everynow and then, but after riding tons of different kinds of horses most of the time I just sit thru them like they don't even happen. I just keep chatting away to the rider next to me, wven when both are horses are jumping around like loonies.