It's also the constant level of activity, not just one self-paced workout a day. Running in formation, chopping on hard flooring, PEP in the early AM and miscellaneous opportunities during the day to exercise + no naps + no sleep-ins + a lot of nervous energy eroding reserves + gung-ho-I-can-do-that = not a lot of recovery time for muscles, tendons, ligaments not accustomed to the non-stop action.
Best advice I ever got before heading off to OCS and similar introductory weeks was "get used to working out on a hard surface." In addition to running, sit-ups, pull-ups, etc., I went out every night after dinner to our concrete patio (in good shoes) and skipped rope, gradually adding time and pace increases. Built up stamina and staved off shin splints, plus doing it in summer heat and humidity of coastal Georgia helped me with the nasty sweat-ex aspects of it all.
As many posters have noted, they will be looked after.
Edit:
Chopping. The pace plebes move at while in Bancroft Hall, the dorm. Double-time trot, center of the p-way (passageway, corridor), squaring corners. The places where they square corners have stainless steel plates in place of the industrial flooring, or generations of plebes would rub a pit in the deck (floor).