First, your problem is on the bottom, so live with it. Your first scratch when you paddle over a rock will be more noticeable. Trying to correct it by sanding just may lead to more blotches and frustration.

Normally, when you scrape edges, the epoxy scraped surface will re-wet out. It's hard to tell from your description if the white specks were there before you scraped or if you created them. I always heat my epoxy to thin it out which helps the fibers get saturated more easily. My suspicion is that your glass was a bit starved. Perhaps you didn't give it long enough to soak before squeeging or you pressed too hard and left it a bit dry. I use a soft plastic squeege and I use it on quite an angle / not too vertical. You are trying to get the cloth to make contact with the wood so it's not floating without squeezing out too much epoxy from the cloth. Be a little more liberal with your epoxy next time, heat it and give it more soak time.