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The only time no problem"could" bother me is when you're paying for an item, you say to the cashier "thanks or thank you" & she comes back with"no problem". She doesn't even look at you. That's when it's very flip sounding.
AC I have never heard 'no problem' used in that context.
A 'thank you' in shops usually elicits no response at all or a 'bye'. But then I don't go in many shops these days.