Sorry your car appears to have been damaged. Carefully check your hinges have not cracked. Also check the strut mounting points have not been damaged. Then with the help of a second person, I would disconnect and remove both gas struts. Then slowly lower the tailgate and let it fully latch closed. What do the gaps look like now? It is unusual for the hinges to move out of alignment, but that is assuming they were tight to start with. My fear is hinge damage. Once you see the gaps you can try to correct by carefully adjusting the hinges. I suggest that you draw around their current position first as this will high light how much you have adjusted their position. Remember there is now no gas strut assistance and the tail gate is heavier than you thing so at least a 2 person job. If you are sure the hinges are good and manage to achieve a good alignment all round take a good picture of all the gaps, only now refit the gas struts and open and close the tail gate a few times. If the gaps have remained constant with the struts fitted then hopefully there was no lasting damage done. All said if it was me then I would look into replacing the hinges for peace of mind.
The marking you can see are to help adjust the hinges to the tail gate so no not covered by the hinges.