I had the soreness after playing rugby, which subsided after a day or 2. I continued to persevere with it, but it turned into excruciating pain during exercise within a couple of months.
Mine was caused due to a grade 2 anterior ankle sprain, affecting all 3 ligaments. I rested for 1 week, then strapped the ankle and carried on training and playing, the lack of mobility in the ankle, caused strain to be put into my knee, resulting in patella tendonitis that I have been dealing with for almost 7 months now.
A few weeks rest, strengthening exercises, and intelligent training has all but fixed it. I keep a diary of the pain, during, and after exercise for however long it lasts, and make a note of the duration and intensity of the exercise.
The idea is to reduce the intensity or duration of the exercise until you get no pain, even for the day after the exercise (even if this means skipping sessions). You then build up to getting pain and/or discomfort, and backing off to an intensity/duration that doesn't cause it. Repeating this gradually will get you back into pre-injury levels.
I started with maybe just 5 or 10 minutes from a 1 hour session. At the very start, I did the warm up exercises with the team, then went home! When I could do this without pain, I added 5 minutes on, and so on.
Give it a go, joint injuries take time to recover. The more you ignore the pain (although it is manageable), the longer the recovery will take when you eventually do have to let your body do its thing.