If it's the patellar tendon(on the front) then it's probably because you are loading the knees too much. Box squatting can really help with this issue IME.
You might try to go a little slower and widen the stance some. Try box squatting and please try to use a proper rack. Squatting without a spotter or a rack is dangerous. Last thing I want to see is you get a cramp suddenly and end up injured.