If you're using a western saddle, your fenders are probably too stiff and not turned properly. Or they could be hung at a funny angle.
The fenders should be soft and supple; able to be easily bent, rolled or folded. When your saddle sits on a horse, the stirrups should naturally turn out as if feet were already in them.
If your saddle doesn't do these things, it may be one of the more economical leathers used in mass production that may always hurt your knees. You can help it some, but it will never be as comfortable as one of a higher quality. Turn Western Stirrups For Safety and Comfort
This was one of the first sites I found with a photo explanation of how to do it.
Another consideration is the type of stirrup you use and where you place your foot. I personally only ride in oxbows, but other members of my family prefer flat-bottoms. There are several other slight variations available that you can check out.
Depending upon your specific event the stirrup is acceptable to be placed anywhere from the ball of your foot to the beginning of the boot heel. I personally find it more comfortable to have a slight angle from the ball across to my pinky toe.