A question of Fishmonger basics and fish processing and handling?
It's common for a few bones to be left behind, so you should always check over the fish before cooking. I use a pair of small pliers to pull out any leftovers. It shouldn't take an hour to clean, though. Any leftover scales should come off with a quick rinse. If the fillet was supposed to be de-boned and scaled, and there were a lot of bones left and scales still attached, that's a bit of a problem.

Did the fish itself smell bad, or was it just the store that had an odor? Did the store just smell a bit "fishy", or did it smell like an environmental disaster? If you're not used to working with fish, you may be a bit sensitive to the smell. Once you get the fish home, you should not smell any off-odors on the fillets.

If you weren't impressed, I would just try to find another place and see if you like it better. It's not a bad thing to have high expectations, and you should find a fishmonger that you're happy with.