There's always a dozen different reasons given for this happening, and the most common seems to be the time between coats.
However, this stopped happening to me when I started to do one thing, and that is to shake the can for a minimum of 3 minutes before using it, immediately before using it. If I'm putting another coat on the next day I'll shake for 3 minutes again. I set the timer on my phone and start shaking.
Someone once explained to me that the constituents of the paint (pigment, binder, and carrier) separate in the can fairly easy and the reason the paint bubbles up and crackles like that is because the binder has unmixed from the carrier (oil or water depending on what kind of paint you have). So if the carrier and binder aren't mixed enough the paint doesn't flow and attach properly.
It made sense to me, I've always shaken for at least 3 minutes, and haven't had that happen since.
Now that I've posted this I'm guessing the next time I paint it will crackle and bubble. Dang it.