The Ready State Virtual Mobility Coach is like having a virtual Kelly Starrett in your pocket.
Are you cooling down after you workout?
Pain is a lagging indicator.
By the time pain shows up damage is already done.
You have less tolerance for deviations in technique following your injury.
You may need to improve your leg position while sitting.
Have you consulted a doctor about the pain that is showing up?
It sounds like a situation where consulting a doctor would be beneficial to see where your knee is at.