Sounds like patellar tendonitis. For the last month or so I've been battling tendonitis that seems to travel all around the knee. I've resorted to using a knee wrap (not very tight, but tighter than I can get with my sleeve) on the affected knee, and that allows me to keep training. On off days, I ice, foam roll, and stretch.
It seemed to be finally getting better but yesterday I felt a pop in my knee when I was getting off the floor and knew it was gonna be extra sore today. It was and I actually had to wrap quite tightly. Oddly enough, there is no pain whatsoever from normal activities: only squatting deep. From what I've read, this is something that will take a while to heal and it might just go away for seemingly no reason.
Also from what I've read, it could be a form issue. Make sure your knees aren't caving inward and/or traveling too far forward, and keep the weight off your toes.
Hopefully, you'll be able to train through it like I've been able to so far. It's a huge distraction for sure.