You can see it on youtube, I just watched it.
In short, Kelly wouldn't give Clay a chance to talk the whole time, from the moment the guest stars (winners of dancing with the stars) came out. Clay jokingly put his hand over her mouth to try to ask his first question to them when she jerked back and said it was a 'no no' and 'i dont know where that hand's been, honey."
IMO.. I dont see why there's a 'controversy'. Regis has done that to Kelly several times during the show. I like Kelly Ripa a lot, but she didn't give Clay any chance at all to say a word to their guest stars. He IS a co-host, and he SHOULD be entitled at least one question, she blasted like 7 questions to them right off the bat and still wasn't stopping, even when Clay was clearly trying to get a word in.