If you haven't put on your third coat yet, the bubbles should be on (or near) the surface. Use a cabinet scraper to scrape them off, then apply a third thin fill coat. But this time, after rolling the epoxy on, slowly drag a dry foam brush (or a dry roller section) across the epoxy, to smooth out the bubbles, before going to sleep for 8 hours.

: Yes, I used a foam roller. I read that using a foam brush or part of a roller
: nap would remove bubbles, I just didn't realize there were bubbles at the
: time. Part of it may have been going to bed after applying the epoxy and
: not seeing it again for 8-10 hrs.