I practice yoga fairly frequently -- a minimum of 2 times per week, usually Warm Vinyasa flow. One pose that I have been unable to get comfortable in is half-pigeon, despite increased flexibility over the past year. It's not just uncomfortable either, it's often painful in my knee and upper-hamstring area. Could this be a problem with my leg positioning or something technical I'm doing wrong?
There are a few adjustments you can try:
If you still have pain or discomfort, try different versions/similar poses, standing supported, standing resting on other leg, standing bent leg lift etc. Modify the pose so that less external force (bodyweight in this case) is applied.
Hope that helps!