So today I opened the back passenger side doors for something and heard this small "tud" sound, I closed the door and opened it again and heard the same. Turns out the back door was rubbing against this door guard clip thiny (first one on page -
Cowles Products - Automotive Molding & Striping) I have installed. I tried it on the left (driver) side and no sound. Then I took a closer look and noticed that the gap between the front door and the back door was wider on the driver side than on the passenger side. Is it just my car or is it supposed to be like that? It's like maybe 1mm wider.
The door guard also scratched my paint in many places when I took it off due to rocks getting between it and the paint, kind of regret putting it on. The only reason I even have it on the passenger side is so that it'll match the driver side, which I need to get out of the car in my garage. Anyway, I just put it back on to cover the scratches.

I'll live with the noise, it's not a big deal and it doesn't seem like it's damaging the door.