Fittings can leak, pintle fixings maybe loose and letting in water.
Also the hull and deck seam on the transom can slpit if knocked but not always noticable, tip the boat up with the water in it so it runs to the stern and see if you can see it coming out anywhere
Final option is screw a schrader valve into a hatch cover, throw in a smoke bomb, close the hatch cover and lightly pressurise with a bike pump, this should force the smoke out of any holes
HTH