So when the ref throws down his bean bag down...that doesn't signal the end of the play?
No. He’s marking the spot where the kick ended for his and the crew's reference. Not killing the play. (Note: the kick ending is not the same as the play ending.)
and waves his hands above his head that doesn't signal the play is dead?
Yes. See my response to Muttly. I believe under NCAA rules the waving of the arms should have been treated like a whistle.
When the ball is resting after a punt and is touched down by the punting team that doesn't end the play?
No. There is no such thing as a kick being "touched down." NCAA there is "illegal touching" which gives the receiving team certain options.
Pretty sure that crew got suspended over that so I doubt that would have happened over a correct call.
No idea if they got suspended, but I highly doubt it.
So the only way a ball is dead after a punt is to pick the ball up and hand it to the referee? I've literally watched hundreds of football games where the punting team downs the ball by touching it when it is just resting on the ground
No. That is not the only way for a scrimmage kick play to end. The ball can be kicked out of bounds. The receiving team can possess the ball, run with it, and be tackled. Complete a fair catch. Be awarded a fair catch. The kicking team can possess the ball. The kick can come to rest and
NO PLAYER MOVES TO POSSESS IT, and a number of other ways. I don't doubt you have watched what you think was the play being killed by someone touching the ball, but that is not what happened.
In this situation the ball came to rest, but someone
DID move to possess it. The ref on the spot jumped the gun and waved his hands. He probably blew the whistle too, but they never said he did. That was the mistake.