Hard to tell from those pictures but where is it leaking? Through that big gap in the side?
It looks like you may have cut the hatch notch too deep or the hatch is too thin. If that grey strip in the second picture is the weatherstripping on the hatch then you have a huge gap to close.
I'm not sure how you are going to fix that other than beef up that part of the hatch.
Also I would have made the long part (the piece sticking out) the fixed piece, not the hinge hatch piece. Water could potentially follow the seam back and leak that way also.
I know our hatches are different but this is how mine looks. The gap is sealed with weatherstripping.



