Not only that, but at the time I watched it I was looking at the replay and I didn't see any penalty in the first place. It looked to me like the sole reason for throwing that flag was to stop the clock. So this morning I went back and watched the play on DVR. I was right. There was no penalty. The flag didn't come out until Brady started to get sacked and the moment he started to go down, the flag flew out. If it had been a legit penalty call, that flag would have went out long before.
The ref ONLY threw that flag in order to stop the clock for the Pats. It was no coincidence therefore, that the refs "mistakenly" didn't run off the time.