It happens. The epoxy probably flowed out of the holes. The easiest way to avoid that in the future (if you're painting) is to use a fairing compound instead of straight epoxy as soon as you're starting to fill the weave. It's cheaper, lighter, easier to sand and does a better job filling the pinholes than straight epoxy. The only reason to use straight epoxy is if you're going to varnish instead of paint.

Check with your primer's manufacturer and see if the primer is compatible with having epoxy applied over it. I know that System Three 2-part High Build Yacht Primer is. If so, you're in luck. Just mix up a batch of fairing compound (epoxy & phenolic microballoons) and use that to fill the holes. Glop it on with a putty knife, then sand it off with a fairing board if you're looking for perfection, ROS otherwise.

If your primer is incompatible, you'll need to sand it off from around the holes, then do as above.

Good luck,

Laszlo