The stereo itself has absolutely zero to do with the hvac controls, but on
some Hyundai models, the controls must be removed to remove/install the
radio, so it's possible that the heater controls were damaged if
removed/installed improperly for radio removal/installation.

I don't know what model you have nor what your specific problem is, so I
cannot tell you how likely it is such an occurrence happened.

So - what do you mean when you say the dealer is blaming your stereo?  Is it
an aftermarket stereo that you installed, or had installed?  What
specifically is the dealer telling you about the stereo causing the problem?
How about a little history of the problem?  When did it start?  Was it
coincidental with anything else that you did?  What are the symptoms of the
problem?