I'm "guessing" with the fiberglass that those fish eyes were from the mold release wax that wasn't completely removed. I know that my Wescott front fenders still had some on them when they arrived, but I did quite a bit of sanding to knock off any gloss plus used quite a bit of wax and grease remover (not the water based type). I didn't have any problems at all with fisheyes.
Another problem that some folks have - using rattle cans of stuff like PB Blaster, silicone or even WD-40 anywhere near (even your neighbor!!) as airborne droplets carry for a long distance. Some are silicone/Teflon base, others just paraffin or oil - and all create fisheyes. Some really don't clean easily with W&G remover - and my guess, the water base wont do as good a job (sorry, BarryK - just my thinking
and I never disagree with you except here) These products are never used in my shop if I'm even considering painting.
Carbon fiber parts - now that sounds like a real pain if you want to retain their appearance and still clean for CC - and I have no experience there.