Question re Penalties and the Clock

Can someone explain the time-keeping rules in the last few seconds of regulation in the East Semi. BC had the ball with 11 seconds left. They ran a play which was whistled down (while in progress) for illegal procedure. The whistle blew while the ball was in flight to Simon (Simon made the catch and it would have been game over from there - it seemed to be a phantom call but that's another story).

Anyway, the clock kept running after the whistle and eventually stopped at 5 seconds when Simon caught the ball and hit the ground. Following that, the refs applied the penalty and reset the clock to 3 seconds. What's the deal? Shouldn't the clock have been reset to 11 seconds if the play was not allowed to take place? At the very least, shouldn't it reset to the time when the whistle was blown?

Never mind... I confused myself with the next play. The universe is still in balance. :oops: :oops: