I had protected sex yesterday and today i have a sore throat, head, back and inner thighs, is this a coincidence or could something be wrong with me?

No STD. Exercise?: No STD or other infection can cause symptoms in under a day. Maybe muscle aching due to vigorous sex or new position(s)? Sore throat sometimes can result from vigorously performing oral sex. But if it's an infection, STDs don't cause such symptoms; it sounds like a cold or something similar probably acquired at least a day or two before the sexual exposure. See a doctor if you remain concerned.