Knee issue's after cycling

I have been road cycling for a year and a half, I have always had a slight niggle with my left knee. I use clipless pedals, but don't think this is the problem now. After I have ridden, usually upwards of 20 miles, two days later my knee gets a little sore around the knee cap, this can last a few days. The pain never starts on the bike.

I had a professional bike fit recently to sort out my riding position. I've had two rides since the fit and the knee pain still comes two days later. However I might not have fully rested the knee before these rides.

Currently I will warm up for the first few miles of a ride, I will have a five minute easy spin after a longer or harder ride. I do not do any stretching after a ride, Would some stretching help?

Any opinions on this are appreciated.