I don't think I've ever had it happen to me, though I never use CW shops so I guess my chances are lower :p I think a minute is long enough, I'd be okay with 2 and even 5, it's an improvement from an hour.
so i bought an item from some shop for a quest, but it sort of failed, then i try again, and succeed. but a few minutes later, i found the failed purchase in my inventory.
so i can see now how one hour cooldown can be justified. won't want double Natasha by accident.
I've found that's been happening for me a little bit from NPC shops lately, particularly when I receive the discount buff while making a purchase. I don't think the shops like Millionaire Center and such really have those problems because there isn't anything extra like that to process during the purchase.