My assumption is that Romo said something like "The guy's helmet came off incidentally." And then Jason said something like "What? Oh."
That said, I don't have a problem with a coach using a timeout to get a discussion with a ref re: a call if the alternative is letting the next play run and having to move on. Even if he did it for no other reason than to make a point that he didn't like a call. Even if he was wrong, it's hardly an indictment of his coaching. One of the strengths of this staff--though nobody wants to admit that they actually have strengths--is that they do a great job with challenges and contested calls. Garrett's a smart guy who cares about the rules. He didn't understand a call, and was willing to use a timeout to get an explanation. Tony, smartly, stopped him from doing so. Not a big deal, at all.
Honestly, you are a smart guy and I don't think you're as much of a blind homer as some of these others, but I don't see how you can watch that and think his original intent was to argue the call with the ref.
I think he was embarrassed Romo called him out in front of the ref on the timeout call and started in about the penalty. I mean, it's not like he ran up to the ref to call timeout and start arguing about the penalty. He called timeout, stood there for a second, Romo jumped in and then a few seconds later Garrett is like "Wait, what? Oh, uh... well, about that penalty call, what the hell man?!"
In general, I completely disagree with your synopsis. I don't see how it is ever kosher to use your final timeout, in a do-or-die game, to discuss a call that isn't going to get changed anyway. You need that timeout to plan your last play of the game, with your job likely on the line, and you're going to instead spend the time arguing with a ref?
And again, it's irrelevant anyway because if Garrett wanted to argue with the ref, he didn't need to call timeout to do it. He was already standing on the field with him, the players were all scattered about. It's not like everyone was on the line ready to snap the next play and Garrett HAD to call timeout to get the ref's attention. The clock was stopped and there was nothing going on. Garrett just lost the moment and went off the reservation.
Thank God Romo was there to save him. Again.