Knee pain with new bike?

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New member
So I just bought a Fuji Roubaix at a shop. Also bought clip-ins. After a bit of riding, I have some pain in the outside edge of the front (lateral / medial) of my right knee. Wondering what are common causes, and what adjustments should I make to my shoes/bike to potentially alleviate whatever I'm doing wrong. Left knee feels fine, both hips feel fine. Only other place that hurts is my crotch from that tiny seat. But that's another story.
 
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