I just found a chip in the tonneau cover directly behind the passenger seat's roll bar. I have no clue how it could have happened. Any else have a similar problem?

 

Check to see if your tonneau cover is level. Look in the post on here about "check your top for pinholes" for information. My tonneau cover looked just like the pics in the message thread and I took it to my dealer to get it adjusted like in the message thread. My dealer contracts with a paint chip repair service and they did a good job and you can't even tell the chip was there.