None of my R9's have hard edges on the trigger that I have noticed. If yours are, then soften them up . BFD, you're not affecting the function of the pistol. If you did have to send it in, I seriously doubt it would raise a brow, unless you butchered the trigger.
To me that would be saying Ghost Chili's gun is no longer under warranty because he cut a few shallow grooves in his mag catch.