I'm not entirely sure what I'm looking at in the photo, but from your description, it sounds like you had some larger air bubbles form. If so, the solution is pretty much what you speculated. Cut the bubbles out and epoxy a patch in, it will be fine. I sometimes just sand the bubble out as opposed to cutting it out, but the fix is easy. If you are worried about how it will look, just sand after it has dried and reapply fill coats until it more or less disappears.