Do a "knee over pedal spindle" test. With the crank extended 90 degrees forward and your foot positioned normally on the pedal, and you seated normally on the bike, drop a weighted line from just below the little point on your knee.
If your saddle is all the way back, the line should intersect the pedal spindle or be behind it. If it's still forward of the spindle, yes, your frame may be too small.
If you're already using a seatpost with setback (1" setback is about the maximum), you may be done. If your seatpost is the type with the clamp exactly centered on the tube, then maybe a 1" setback post will help. They're common and not expensive.
What's your "cycling inseam" measurement, and how long are your cranks? Occasionally too-long cranks can contribute to some types of knee pain.
RichC