One thing I can think of is amine blush. The epoxy should be scrubbed with a scotchbrite pad and water then rinsed well before the anti fouling paint is put on. This might be the problem.
Couple of things to add.
Brian's probably right. If the amine blush wasn't removed after that last coat of epoxy had cured, then this could be the cause of your water ingress.
If you want to dave yourself some time & effort next time you do the fair/fill kibuki dance, try using cabosil/colloidal silica as a thickener. You can probably completely fill your craters in one go.
If you elect to go without cabosil and go the multiple coats of unthickened epoxy route, don't let it fully cure before you apply the next coat. As long as it's still soft enough to "grab" the fibers in a cotton ball (or you can indent it with a fingernail), it's ready for the next coat of resin without further prep. This is actually preferable to letting it fully cure, since you'll achieve a chemical bond between the layers instead of a mechanical one.
If it gets too cured for the above, then let it go to an almost full cure. Before you have at it with sandpaper, like Brian said give it a good scrubbing with a green ScotchBrite and water, then rinse well. This will remove the blush that accumulates on the surface of the epoxy. Then sand it for the next coat.
BTW, if you've removed the blush from your surface layer of resin you won't need to do it again next time you sand/paint.