Hi, it's a bit hard to tell from the photos since one looks like a medium broadcast. while the other one looks more like a full broadcast.
In any case based on your description they may have applied the flecks later than they should have since if the epoxy started curing and hardening they won't 'sink in' to the floor so instead they appear to be sitting on top of the floor quite a bit, or went in sideways and didn't flatten out into the coating. Most definitely they should not crunch, be loose, or be dangerous.
The way to repair this is to run a flat floor scraper hard over the floor to remove and knock down the high spots, and then recoat with clear and nonskid. Have them do a test area in a corner first to make sure you are pleased. If they can't fix it to your liking then it needs a good sanding or light grind, re-epoxyy, re-fleck properly, and re-topcoat.
Topcoat is a thin coating and will do little if anything every to 'fix' problems with the floor.