The gas struts that support the hatch put a massive strain on the hinges/ hinge mounting and can result in the hatch not closing properly. I had this happen. As a temporary get me home solution I removed the gas struts and the hatch would then shut.

Tailgate hinges
 

I have a pair of tailgate hinges in primer with stainless steel pins if anyone needs them. These should stop them going stiff and bending the mountings in the roof beam