OK, so, I watched that scene about fifteen times with my volume to the max and focusing each time on just one of them. Ennis' mouth is completely closed, shut, lips zipped together when the supposable "I'm sorry" is uttered. On the other hand, one can see Jack's mouth move slightly, not too much, since, at the first "It's alright" he barely whispers. You see his mouth move again, the same way, when the second "It's alright", more distinct, is said and then the third one is really clear.
As much as Ennis saying "I'm sorry" makes sense to me from a logical p.o.v., I neither heard, nor saw him saying it.
Tried to hear the "Lie back. Come on.", but all I got is some undistinguishable whisper/breathing, that kinda sounded like "Lie back", but no "Come on".