I am using Entropy Super SAP CLR with a slow hardner.

I'm not familiar with this epoxy. EVERY epoxy is different! Every material is different.

we laid out the fiberglass and applied a fill coat

You wet-out the glass AND then applied a fill coat, or just wet-out the glass?
Did you squeegee excess resin off the glass?

I waited 4 hours and applied a second coat

Was the glass tack free after 4 hours with a slow hardener? That is a fast set-up. Epoxy manufacturers make many epoxies not all of which are designed for a transparent lay-up. If price is your first concern, the cheap epoxy may not be optimal for a transparent lay-up. A fast setting epoxy will allow less time for bubbles to rise and dissipate. Using warm temperatures to thin a regular viscosity, fast setting epoxy (MAS), will not allow bubbles to rise and dissipate as well as a regular viscosity, slow setting resin (System Three).

Coating thickness can be another issue. An experienced epoxy user applying thin coats may not have the same problems a novice has applying thick coats, using the same resin. Epoxy looks thick, goes on thick, and fools novices every time into applying too much, which runs, drips and sags off the surface.

Did you apply the second coat using the slow hardener or a medium or fast hardener?

If the bubbles appear to be on the surface, I'd suggest using a SHARP scraper to remove them, over sandpaper which will clog up with the green soft resin.

Rob