while doing squats our complete body weight is there on our legs and knee. may be you get pain after sometime. and in the begining every one think it as painful as time goes and you get used to with it then you will not feel it as painful.
I think this is muscular pain which you are facing and this will go after taking some rest from your exercise. So do little bit exercise from this part and try to contact with any doctor may be there some sprain.
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Pain of sudden onset on the top of the foot just behind the toes, without a history of trauma, may be due to a stress fracture of a metatarsal bone. There is usually swelling in the area and it is painful to the touch. A history of prolonged walking before the symptoms began may be present.