I've talked to a few E93 owner and they never had this problem on the vehicle. I took it in for a clunking noise on driver side turn out to be a latch problem, they did a minor tweak on the roof and this problem pops up and never going away. The weird thing is squeaky & clunking noise came in at night but not during the day.
I had this problem when the car is not even at 1K miles.
14 F30 335i M Sport Melbourne Red
13 E93 M3 Melbourne Red
12 E93 Space Gray ( Retired BMW buy back )
2006 E90 ( sold ) 09 E82 Space Gray ( sold )
My next vehicle would be a Zamboni