Nah. If you were overextending, you would feel pain in the BACK of the leg from overstretching the tendons- like in the pit of the leg. Pain in the front of the leg- the knee could mean that your seat was too LOW. Riding with the seat higher actually will give you more power in your pedal stroke, so it is always better to have your seat a little higher vs. a little lower. Still, it is BEST to have your seat just right, so I would definitely recommend finding a bike shop in your area that can do bike fit measurements so you can alleviate any more problems.
For knee strengthening activities, do stuff like squats, lunges, the quad extension machine, and the inner/outer thigh machine. Strengthening the muscles around the knees will help protect and strengthen the knees.