Why do my feet hurt when i do jumping jacks and box jumps etc?

One would have to : Examine your feet to answer the question. You can try looking at your feet while standing and looking in a mirror to see if you are flatfooted as the jumping may be putting additional stress on the foot and /or perhaps wearing an orthotic would take some stress off the foot during these activities.

See below: It could just be from the pressure or jarring from the exercise themselves. Try using a gel innersole in your shoe to absorb the shock.