It sounds like they waited too long to scatter the chips so they stuck to the epoxy but didn't lay flat. They'll probably wear down, but then you won't have the full effect of the chips.

Laura. You can still get a nice finish out of it. Definitely call them back because from the way it sounds from your post, a topcoat was not applied. To fix it yourself; go over the surface with a metal floor scraper or metal snow shovel to break away pieces that are sticking out. Really take the time to go over the entire surface and don't worry about leaving scratches because the next step will remedy it (just don't get too carried away as to gouge out a piece of the surface). After you break them down, vacuum and really sanitize the area from dust and debris. Then, apply a clear, epoxy topcoat. Good luck!