I think you're misunderstanding the role of the hamstrings in the squat. The hamstrings primary role is to support the back angle in a squat. During the part of the Range of motion where the back/hip segments are dealing with the most moment force from the bar, the hamstrings are not changing length to any appreciable degree, and are therefore not exposed to much eccentric loading. Eccentric loading is the part that produces DOMS. If your hamstrings are sore, you've either misinterpreted the movement instructions, or you're allowing some part of the bottom of the movement to turn into a goodmorning. Post a video.