One explanation could be TMTS (Too Much Too Soon) syndrome, which are very common with flat feet runners attempting to train a race. With that being said, as I mentioned earlier, the two principle components of foot function are the motions of pronation/eversion and supination/inversion. These two mechanical components are the ankle's ying and yang. Although a recent 2010 study suggests that flat feet may not be a factor in the development of TA related injuries (1), I find
Typically with flat feet, overactive and underactive muscles propagate mechanical imbalances and musculoskeletal abnormalities which lead to multiple foot and ankle injuries. I have first-hand experience, genetically speaking, I am prone to ankle sprains and strains with different severity. Once, I broke my 5th metatarsal due to a minor ankle roll as I was simply walking on an uneven surface (yard).
Overworked and overly tight muscles: