1) surface not clean enough (besides thorougly removing all old paint, dust the surface with one of those microfibre mops: they do wonders!);
2) wrong mixing of the two components;
3) apllication with an "orange peel" roll;
4) application of second layer before the first one has thorougly dried;
5) too much "pulling" of the epoxy while appling it or too long strokes in applying it.
Epoxy does fisheye very easily and it also leaves pinholes unless you are very careful. One problem I found was silicone - removing the rubber sealant from the windows left a dust of silicone all over and it took ages to get rid. And other materials can carry this - brushes for example, or rags.
Epoxy should be stored in the warm to prevent crystals forming. Check the bottom of the bottle, and warm to disolve.
Any crystals in the epoxy mixture will leak and form fish eye depressions. These areas will be 'waterproof' to any additional coats. Small crystals can also cause problems. Probably the best way to treat fish eye is to break an all hard hacksaw blade and grind into a curve to match the fish eye. Lean the blade towards you and pull while pressing down. It will rapidly remove the epoxy. Sharpen about every 10 minites. It's action is similar to a cabinet makers scraper, far faster than wet & dry.
The saw blade is also excellent for finishing epoxy fillets. Best used before the epoxy has reached full set.
I would bet my last penny your problem is contamination, sounds very much like Silicon to me, try using a silicon remover first and stop polishing the boat with silicon type polish, you will find the same reaction with most paints.