Make the doctor do his job.
But it is possible that something you've been doing over the last two months has changed. I'm going to use punching as an example. When you first started, you probably threw your punches with much of the same muscle, and a little more technique than when before. But as you learn more and develop more skill, you'll start using different muscles or the same muscles in different ways, and also putting more effort into it. Which can sometimes cause injuries -- both stress and overuse. Another thing that can happen over time is that bad habits can creep in and cause injuries. For example, I took a good principle of rolling my shoulder, and overdid it. I ended up with sore shoulders...
But don't rely on an internet board to diagnose you, and don't settle for a doctor who's blowing your concerns off. He may be right, and it may just be a tight hamstring (not an uncommon cause of knee pain) and lack of stretching. Or it may not. Either way, YOUR concerns aren't eased, and that was his job.