Sometimes they stop them early, sometimes they stop them too late. Sometimes fighters are just punching so fast, that by the time the ref gets into position to pull the guy off it's just too late.
This could be helped with better positioning but other times it's just a case of the referee is just simply not able to get there fast enough due to the laws of physics.
Alot of time we blame the fighters for throwing extra punches. But you don't know what it's like to be in there. Your brain can be in reptilian mode with a kill or be killed mentality. That's why there is a ref.
Steve Mazzagatti was amongst the best refs we ever saw in the business. Even Dana hailed him as a good friend.