The dealer can blame you if they want but you can protest with BMW NA and/or go to another dealer. A burnt coil at 3k miles may be blamed on launch assist or a money shift the rev limiter couldn't handle so beware. I know this because I had to replace 2 coils on my wife's 325ci and they claimed it was from abusive driving habits, which I asked them to prove. In the end, with so few miles, it must be defective.
on another note, why tear off a part of the stock system so early? Your drivetrain has had no time to break in. I would be concerned with longevity.