What was your training like, 3 months ago? What were you doing that lead up to this?
How is your squat? Do you use a super narrow stance with lots of forward knee drift?
What rehab exercises have you been doing?
When my legs were at their weakest, my knees/patalles hurt all the time. I had so little muscle, my body tried to "bounce" like using my patella "jump" through the motion instead of driving the squat with my leg muscles.
I did lots of Peterson Step Ups, Terminal Knee Extensions, Step Ups and Lunges to try to train my thighs and knees to work right.
My glutes and hamstrings needed work too.