My rear hatch doesn't close completely.
Latch on bottom and latch on door works perfect.

When it closes, the system think it's closed. no light on.

The issue are it looks ugly and come out cold or warm air from it when a/c or heater are used.

Is there some way I can adjust?

I tried to unscrew bolts and adjust both latche positions but no space to move around either bottom or door latch.

Is there some way I can adjust?

 

Hard to tell from the pics but it almost looks like it's bent in the middle. Any accident history with the car that you know? Does it line up at the top and bottom but just stick out in the middle?

 

No accident history.

Bottom also comes out.

Top goes in little bit.

Looks like it just requires to push more.

I just don't know how to.

All latches works and when the tailgate is closed, I can see the tailgate is pulled by bottom latch little bit, just not enough.

 

If the gap is even from the midpoint down I'd say the latch needs to be adjusted to close it tighter. I know I've seen something out there but I'm not finding it at the moment. I'll keep looking and see if I can find something showing you how to adjust the latch to close it tighter.

 

This will sound stupid but you have checked to see that nothing is blocking it from closing fully right? Sometimes it's easy to overlook the simple solution.

 

It looks bent...

 

The adjustment is at the top. It is a combination of where the hatch hinges bolt to the hatch frame and where the hinges bolt to the body at the roof. You will need to remove the inner rear window surround trim, the glass and hatch lift struts ( to relieve tension ) and the plastic trim covering the rear hinges.
I had my CTT @ the body shop a while back and the rear hatch was replaced. However, when I got it home it looked just like yours. I had already talked to them about correcting it when I inspected it before scheduling pickup and their excuse was " thats the way it bolts together from the factory". Realizing that the battle was futile and I would do it myself, and already having a tow in place for the two hour journey, I let it slide. This is how I came to learn how to adjust my hatch.
There is a small possibility that the trim piece is not being retained properly causing it to bow out. The hatch assembly with all the trim and glass is super heavy, know this before you start loosening stuff and it falls down. There is no adjustment @ the bottom latch. You need to first adjust the hatch-to-body fit ( you may need to adjust a combination of the hinge-to-body/ hinge to hatch ) and then the glass-to-hatch fit. Last, adjust the little spoiler on top to the hatch and body. There is a hinge on either upper side for the hatch/glass. Each hinge has two arms and serves a a dual purpose. Good luck, its a job.