During "Smells Like Nirvana", when he goes to do the gargling, you can see the cup in is hand, then back on the stage in front of him, then it's back in his hand.
DUH thats obviously what they did because they can't use computer graphics or crap like that in live concerts that kind of crap is seen in NYSYNC concerts all the time
A lot of times when a "Live" concert show is made, whether it's for a video or a TV broadcast, they use clips from different concerts. The pick the best shot/ angles and edit them together with the best sound track. These kind of things happen all the time.
When I saw Al live in April 2004 he had two cups. One in his hand which he gargled with and one on the floor which he kicked at me and my friends. That's probably what happened. I'll have to go watch the DVD to be sure.