You can cut the bubbles out with a matte knife and keep right on chugging along. You could patch them but they are small enough not to matter. Subsequent fill coats will probably hide most of the blemishes.

I don't know what happened but from your description I would do things a bit different... Mix your epoxy well. I pretend I am scrambling eggs. Chuck a batch if you think you might have mixed it wrong. Glass after the sun sets below the horizon; rising temperatures can cause "outgassing" of the wood pores (bubbles).

Don't sweat it unless the epoxy never hardens - that's when you know you screwed up