Once the timeout was called, the referee blew his whistle and came running in from the sideline. When a whistle is blown the play cannot continue, even though most players didn't know it had blown. This applies to all areas of the game. For example:
- An interception returned for a touchdown that is originally called an incomplete pass may be overturned to an interception, but only at the place of the catch.
- A recovered fumble that is returned for a touchdown in a similar fashion to the interception case.
- A play being whistled dead for a player stepping out of bounds.
These plays have to do with challenges or reviews, but emphasize that if a whistle blows play dead, the play cannot continue. It is a player safety issue as well as competitive balance issue for any players that hear the whistle and stop playing.
NFL Rule 7 - See Section 2 Article 1
The best way to look at it is: If a whistle blows, the play is dead and anything that happens after doesn't matter unless you're talking about a personal foul penalty for some reason.