Two videos contain rare apologies by pitchers. Both are the innocuous "my bad".
8/5/14: Joba Chamberlain hits Derek Jeter with a pitch, then apologizes to his former teammate
8/12/14: Chris Young apologizes to Jose Bautista for throwing a pitch high and inside
Joba displays obvious and immediate remorse for hitting Jeter, especially since it happened in Yankee Stadium. Young is much more subtle about a previous unseen pitch that missed Bautista. In both cases an announcer tells us what the pitcher said.
Neither batter seems to acknowledge the gesture.