Could be a cratering problem. It's a problem that mainly appears when recoating a sanded epoxy surface. The craters appear as pin-head sized craters. It's explained in SystemThree's epoxy book, (although it doesn't seem to be a problem with their epoxy). I'd be interested to know which brand of epoxy you used.

It's also one of the reasons that it's best to apply the fill coats without sanding in between, while the previous coat is still "green."