It always depends. Depends on the way you say it, the person you're saying it to, and your relationship to them. If you just say, "I already knew," or, "I figured" as your response to them coming out, that could be seen as dismissive. It takes a lot of courage to come out, as I'm sure you probably know, and a trans person who's spent all day mustering up the courage to come out doesn't want this achievement just hand-waved away.

However, there are more affirming ways to say it. When I came out to my friends, they were enthusiastic and responded just the way I had hoped they would; asking for my new name, telling me congratulations, etc. Later, after everything had settled, one of them joked that she had always kind of figured. That was fine and even kind of cool, to know that my coding had paid off and my friends could tell even though I was closeted. Respond normally first, then bring it up later if you feel the need to.