No - I don't think your sights are set too high. You mentioned you've seen pics on this forum showing great member floors, now keeping in mind that most of those pictures are from DIY projects, it's certainly reasonable to expect at least that level of quality from a contractor who's getting 3x or more the $$$.
Sorry, I'm not familiar with the specific product used on your floor, don't even know if that clear is a urethane or epoxy, but can say that I'm not aware of many contractors who use that brand.
Sometimes bubbles are caused while mixing, other times by concrete out gassing (although that's usually for the initial coat only), sometimes by chemical reaction while curing. But whatever the cause, generally bubbles can be mitigated by taking the appropriate actions early on.
The contractor not cleaning up that trash when you pointed it out, and then coating over it, is amazingly irresponsible. It's time to have a heart to heart with him.