This is the correct answer. Increasing volume too quickly while not stretching will cause this sort of issue. Stretching is more important than people think if one is putting in decent hours on a bike. It can be made worse by a poor bike fit/haphazard cleat adjustment, and cold weather. If your cleats are aligned wrong, you'll feel it on the outside of your knee more than the inside, as that controls lateral movement. If your seat is too low I do believe you'll feel it on the inside of the knee.

Observe your pedal stroke while riding- is your knee tracking straight up and down, or wobbling side to side? When your foot is in a neutral position, do you have float available to twist your foot around in both directions (you should)? Do you feel hard efforts mostly in your quads, not in your hamstrings? Do you drop your heel at the bottom of the stroke? Do you have to point your toe (as in, are you "ankling")? These are all things to consider when making sure you're well set up on your bike. I tend not to give a **** about the KOPS fit, as all the things I just mentioned require different adjustments for different people.

To reiterate- You should feel your quads and hamstrings engaging when you pedal. Your lower back should be mostly straight. When sitting and not accelerating, on a climb you should be able to relax your upper body and not lose power. You should have float available to both sides of your neutral foot position to avoid putting side stress on your knee. Your heel should not drop, but you shouldn't have to point your toes, when your leg is fully extended. Bar position is determined by how flexible you are and what you feel comfortable with.

And learn some stretches.