That makes no sense. Who would call a timeout to see why the clock is stopped?
Romo didn't interject to say, "Don't call the timeout.", he interjected to say, "Don't call the timeout right now." They ended up taking one, the whole point was to let the clock run, so yes, it was running.
Not to rub salt in Garrett's wound but...
What actually happened was the clock was stopped at 1:42 when Garrett tried to call the timeout. The refs had just gotten through sorting out the helmet thing and had not restarted the play clock yet.
I think what happened is Garrett completely forgot the previous play was a run and that the clock was going to restart, so he called timeout to talk over the 4th down play. The clock was still stopped at 1:42 at this point.
That's when Romo jumps in and stops him, and I'm guessing points out to his coach that the last play was a run, and that the refs were about to re-start the clock.
Garrett then uses the next 25 or whatever seconds to yell at the refs about something. Maybe the penalty, maybe something else, who knows? But it's clear as day to me that Garrett thought the clock was stopped at 1:42 and was calling timeout to talk over the final play of the game before Romo stepped in.