LeeG mentioned that it may be off-gassing caused by a rise in temperature. This is possible, but less likely given that it is the second coat.
If you used a foam roller, it may be the cause. I noticed on my first boat that these would show up after epoxying. They are there on the boat, but not noticeable untill they are 'dry'. You can use a foam brush to remove these, just lightly 'scrape' the surface of the setting epoxy. I do this about 5-20 minutes after finnishing with the rest of the epoxy (depending on temp, epoxy type, etc)