Why is there damage on chainring like this as well as on frame?

Factory new Trek Madone SL6 Gen 7 (Never rode)
The chain was never really feeling smooth (During checking)
I set up the 105 di2 completely again and still found a bit of residual issues, so removed the crank and chainring and noticed that the inner of one of three plates is having rubbing issues (rest 2 are smooth). The inside of derailleur has its own rubbing issues and the bike has minor paint damage near the bottom bracket part. Can someone help resolve this?

by YatharthIMA