Even then you don't go "you don't understand x!". You make an actual point about something in the presentation, usually with enough self-doubt to state it as a question.
If the whole presentation is trash in your opinion, just leave.
Also, if someone just says "you're wrong about X" that's way easier to deal with than "considering this other paper says these things, can you explain your motivation for X?".
I find that to be the other way around. I would much rather have people ask the second kind of question, whereas the first kind will give me nothing to work with. In the worst case you can answer that you havent read thtose papers and you will after the presentation. At best they can actually teach you something you haven't considered yet. But often you can respond with your motivation which you generally thought about for much longer than they did.
Most researchers I know welcome difficult questions. Like that's the whole game. Finding the difficult questions about your work and answering them.
A lot of the time, it sucks of you only get bad questions or no questions. It usually means your work was uninteresting or so poorly presented no one grasped enough to even ask about something relevant.