it's time to take a look at the mid foot and subtalar joint (STJ). During movement the foot can be an active shock absorber via muscle activation to decrease impact with the ground, this happens when the foot 'unlocks' by pronating. During a squat, the foot pronates due to coupled motion at the STJ. The tibialis posterior muscle plays a large role in decelerating foot pronation and navicular drop. With flat arches, the foot is already pronated. If rear-foot dorsiflexion is limited during a squat, the mid-foot may excessively pronate, lengthening the posterior tibialis. Constant lengthening of a muscle puts it at risk for tendinopathy and a biomechanical disadvantage leading to weakness.
Dorsiflexion could be limited due to the plantar flexors being tight or the joint capsule limiting the motion. Increased pronation at the foot can alter foot mechanics and even lead to increased internal rotation up the kinetic chain! Here is a video demonstration of the movement pattern mentioned above followed by a corrective exercise to strengthen the post tib in the right manner.
Described by Kulig et al 2009 (non-surgical management of Post tib tendon dysfunction) performing eccentric exercises for tibialis posterior may benefit individuals experiencing early stage tendinopathy. Be sure to use your hand to place the foot in plantar flexion and inversion - "point your foot down and in"