Sometimes you can feel more on the tibia then in your patella. Probably your tendon is still injuried since you didn't have a proper treatment. There is another possibility of patela-femural disfunction (which is multi-factorial, but you should go to a physiotherapist for a proper assessment and orientation. It's impossible to diagnose someone like this.
I can give you one orientation: whenever you are doing squads dont let your knee pass your toes (this will force your muscles and not your joint and tendon)