Okay, now that people have replied, I guess the "sorry" that some people hear is not just another " 's all right" by Jack.
In that case, I have another theory, and it goes along with Jack's "f*** me" and Ennis's "I love you," as well as Jack's "sorry."
In each case, these are unscripted lines that were added by the director/actor as motivational cues. They are not necessarily meant to be heard--they are meant to be felt and observed. Sometimes when an actor acts, he or she has a "motive" for each important speech or scene. For example, when Heath embraces the shirts in the last scene, saying, "I swear," he (or Lee) has told himself that the fundamental motivation behind the scene is his deep love for Jack. So he's trying really hard to get that love across, and (not even intending it to be audible) exhales the words "I love you" as he's acting out that thought.
Likewise with the tent scene: Heath got it in his head that he's supposed to be very humble, very apologetic as he enters. He is projecting this through his demeanor, and he (consciously or uncosciously) breathes the phrase "I'm sorry" as part of his acting.
I'm not going to get into Jack's motivational thinking during the FNIT.
There is a technical name for these added lines that help with the feeling/motivation. In stage acting, they are generally understood to be said under one's breath so as to be inaudible to (the vast majority of) the audience.
Now I can't remember that technical name.... But I've convinced myself that's what these "phantom lines" that some hear are.