This might be a stretch (no pun intended), but let me know if my theory is valid?

I use a Specialized Phenom in 143. I've been getting knee pain recently, and it's not my saddle height or cleat position since I haven't changed those. I have been riding more frequently and notice that my hamstrings are hurting. I think because they are hitting the edge of the saddle. Could this in turn cause my hamstrings to pull on my knees, causing pain?