If they are willing to lightly sand and apply another topcoat free of charge I'd go for it. I always recommend a minimum of 2 topcoats. Poly is so thin 1 coat is just not enough imo. And hopefully they do a better job of rolling it on with another coat.
How many topcoats of poly did they do? 1-2 topcoats you shouldnt see roller marks if done properly. As it gets some foot traffic it will be way less noticeable though.
I would be pissed if a company did that poor of an install. That needs to be redone or at a bare minimum a second broadcast of flakes. At $4.50 per SQ ft you can't expect too much though. That is very cheap for a proper flake flooring job.
I have installed many epoxy and poly aspartic flake floors. First of all, $2500 is extremely cheap for a 3 car garage, so I wouldn't expect a very well done job to begin with. That is a very poor install. Don't let them fool you. A good install should never have loose chips, sharp edges or...