Ive noticed millennials will try to class up their "no problem" by upgrading it to a deliberately punctuated "not a problem." Marginally better thanks to the additional effort, but it still falls flat to my ears. Like, I know it wasn't a problem. It was as easy as handing me a pen and I watched you do it. Is pointing out the obvious all you've got? Do you not care either way in helping someone or being appreciated for it?
When it comes to brief, casual interactions with people like store clerks, it's all pro forma niceties anyway. It's remarkable how many clerks don't reply with ANYTHING, and don't really even pay attention to the customer while tallying up their purchases. I don't expect chattiness, indeed I dislike that, but it is both professional and efficient for the clerk to focus on the customer for the duration of the transaction. So, if I say thank you, any reasonable reply is fine: you're welcome, no problem, any time, etc. I find when a clerk says thank you to me, he/she is also often handing me something, either my change or my purchases, so I end up saying thank you as well, for the item being handed.
When replying to friends or coworkers in more significant situations, I will very much tailor the response to the situation. I tend to say "not a problem" (yes, that variant), or "any time", or "my pleasure", much more than the standard "you're welcome". Occasionally I will elaborate, as in:
Other person: Thank you for helping me do X.
Me: I'm actually glad you asked, because it gave me the opportunity to refresh my memory about how to do that myself.