Hello Matthew and thank you for posting this here.
I'll assume you're a 25 year old male in otherwise perfect health who is getting plenty of rest, eating organic raw fruits and vegetables, and avoiding caffeine, alcohol, tobacco, and refined sugar.
Obviously self-diagnosis merely resulted in a costly MRI and a perfect knee. Ah, what price perfection.
There is a difference between yoga asanas (poses) that provide hip opening and ones that require hip opening. Unfortunately the person who directed you doesn't make this distinction. Sitting crossed legged (was it with the feet in the crease of the groins?) requires hip opening, it does not deliver it.
While I'm not a doctor and my feedback should not be confused with medical advice, what can happen in the circumstances you mention is that the medial collateral ligament can be stretched. It's rarely (if ever) a good idea to mobilize ligament in this fashion. I don't know that this would be revealed in an MRI though a mobility test from a superior ortho might discover it.
That sort of thing would not likely respond to an IT stretch. So you may, in fact, have something else going on functionally. There should not be any sharp pain in a joint.
See a therapeutically trained yoga teacher.
Apply Sunbreeze oil to the knee joint every two hours.
Organic, untoasted sesame seed oil to the knee once in the a.m and once at night.
Learn to properly contract your quadriceps.
Stay hydrated - consume at least half your body weight in ounces.
Rest frequently. A 3 minute savasana every hour.
Find some MSM or other joint formula at the local health food store.