I was having a serious issue with my roof liner making loud creaky/squeaky noises. The worst was above the driver's side handle. I dissassembled some of the roof to take a look. I am pretty sure it is two things.
First is that there were some old factory stickers that were all dried up and debris that came in through the sunroof. That was pretty easy to clean out.
Second, I think that roof liner itself is just poorly made. It really only started to make the noise when it got hot outside (80F+). If I pushed on it while driving, I could make it stop for a while, and usually when the car cooled down it would also be minimized. I took a trick out of the audio world where you add some mass and elasticity to absorb vibrations. How? I used some very high-quality Gorilla brand duct tape. I applied it in long strips and overlapped it where I could. I did this down the entire length of the driver's side and as far in as I could reach and apply tape.
This seemed to complete eliminate all of the noises on the drivers side. It has been in the upper 90's F here the last few days, and not a single sound from that part of the roof!
Hope this helps.
First is that there were some old factory stickers that were all dried up and debris that came in through the sunroof. That was pretty easy to clean out.

Second, I think that roof liner itself is just poorly made. It really only started to make the noise when it got hot outside (80F+). If I pushed on it while driving, I could make it stop for a while, and usually when the car cooled down it would also be minimized. I took a trick out of the audio world where you add some mass and elasticity to absorb vibrations. How? I used some very high-quality Gorilla brand duct tape. I applied it in long strips and overlapped it where I could. I did this down the entire length of the driver's side and as far in as I could reach and apply tape.

This seemed to complete eliminate all of the noises on the drivers side. It has been in the upper 90's F here the last few days, and not a single sound from that part of the roof!
Hope this helps.