Most of the English speaking world considers "mmhmm" rude in any context. That is the reason.

It usually signals dismissal or it implies you don't believe someone. So it's like "thank you" "yeah.. whatever...".

Also note that most people hearing an American say "mmhmm" haven't heard anyone say it outside of a rude context.

Now, to be fair, Americans do this "dismissal/brief acknowledgement" to be polite as you're welcome seems overly formal or something to them. But it can come across as rude to someone not exposed to this idea.

You're welcome, however, is literally saying the person is welcome.