my rear hatch does not line up flush with the rest of the body when it is shut. it is higher on one side than the other and the hatch hangs off the back by an inch or so. here is the only picture i have of it right now, but i can get more if needed.

 

there are 2 octogon shaped rubber bumbers that screw into the hatch, you might want to check the drivers side one and screw it all the way in. Also check for any damage. People shut their hoods and trunks with tools lying in the way all the time.

to adjust the hatch inward towards the body, you need to disconnect the hatch shocks, find a friend to help with the adjustment. Then loosen the bolts at the top of the hatch and push in towards the body tighten bolts and lower it down to check the fit. You might have to do this a few times to get it right.

The pic you posted looks like the quarter panel has been hit, if it has been hit before and improperly repaired that may be the problem.

 

i had to change out my rear decl and wow it was semi easy comming off but i could not get that back on to save my life , i had to bungi it down and bring it to a body shop to help , they had to change off the latch with the old one and de gunk the window tar from the new/old hatch i put on costed me 125 but i would have been there for weeks tring to align it right

 

it was hit, but very minor. my brother backed the side of the car into a 1" metal pole and it just bent it in. i've already mostly popped it out. it was misaligned before he ever did that.

 

I found it is a lot easier to align the hatch with the struts off. Then i loosened the bolts and adjusted it to the body lines, hooked the struts back up and then adjusted the plastic stoppers on the back for height.