Honestly, the only time I see clean cups in my local Petco is when they've gotten a new shipment.
The thing that upset me the most the last time I went was the baby bettas section. There were probably 10 cups and only TWO of the babies were alive - and even those didn't look very good.
I'm actually going to write to their corporate office about it. I've gone into that Petco and seen 5+ adult bettas dead (and moldy to boot), those babies were pitiful and all of their fish look unhealthy. Do they really expect that people will buy a fish that looks sick and dull?
All of my boys (save one that came from Petsmart) have come from Petco. My local store doesn't take great care of their fish, but they have a ton of different colors and tail types.