It really depends on the phrasing of it. "I'm confused, why on earth did you write that web app in perl in 2017?" does certainly come across as condescending. "I'm confused, we don't usually use perl. What's the benefit here?" opens it up for a discussion.

The secret, I've found, is to assume that everyone is doing their best with what they've got. Everyone has a different set of information, background, experience, etc. Maybe you'll have an opportunity to teach them something; maybe they'll have an opportunity to teach you something.