Knee pain can be from so many different things. i have had knee problems while cycling for ever it seems. My seat foreaft position was the problem!! gah! Anyway, knee pain after exercise can be for a number of reasons including tight muscles. Try stretching (gently, with NO PAIN) your IT band, hip flexors, quads, inner thigh and hamstrings. Each of these muscles "tugs" at your knee in some form which can cause some pain in your knee. Definitely get assessed by your physio or doctor.

good luck!

Han