Heh, he actually probably was. Obviously not as part of a conspiracy, but the hand signal Brady was giving is an officiating signal for "reset the play clock to 25 seconds" which is given after certain play stoppages where the clock is supposed to stop running. Brady was probably using this signal to let the officials know that they forgot to signal for the play clock to be stopped and needed to reset the time.
Incredible that anyone would mistake it for some sort of play clock conspiracy though haha.