I'm not sure which rally you saw footage from but McCain was in Lakeville, MN yesterday. As McCain likes to do he takes audience questions. There was a elderly woman there and McCain went over with his mike to take her question. She started to say that Obama was an Arab but McCain cut her off and took back the mike. McCain told her Obama was not an Arab to which you could just hear her say faintly, "Oh, he's not?" McCain replied, something to the effect, "No ma’am he is not, he is a fine family man..." He went on for a bit then about Obama.
IMHO, in this situation McCain did the right thing.
Now, that being said, there are some accusations going around that the Obama campaign is sending plants to McCain rallies to stir up troubling negative comments in the audience as McCain and Palin speak.
Take it for what it is worth – a rumor.