Although pain is below knee but your history suggest due to over-squats, front thigh overuse; is giving you pain at back of thigh. If you do any exercise of front direction as squats, then either you have to balance by doing equal Exercise in back eg hamstring curls Exercise/ opposite side muscles use ; or do streching Exercise of same side I.e quadriceps. Lack of warm up, cool down and lack of streching is the main cause of your pains. Secondly lack of core strength is another reason of pain.
In squats quadriceps works a lot and shrink in size to elongate this muscle again, do it's strech
Do strech your quadriceps for best outcomes.
Link to strech this is given below
https://youtu.be/ZpBCCJPeqFY
Do this and don't forget to make an online appointment to learn exactly the Exercises to make you feel better. Warm up, cool down and more.
Next Steps
Understand your workout, don't just do anything; as doing any exercise is not going to serve the purpose. I have done study in Sports rehab from Olympics Strength trainer (America). Therefore, I could guide you better; your 'body specific' demands of Exercise, warm up, cool down, your priorities; to know more contact me.
Health Tips
Don't do any sort of workout, but do specific to your body; what your body and your goals demand from you. To know more visit a Physiotherapist, to guide you in specifically designed protocol for you.