uh ... no. He was simply scratching his face.
I know several males who do that to express “the bird” furtively.
But they’re all from Arizona, I don’t know why. Maybe the people who cheered in the audience were from Arizona...
Anyway, take a look at 2:50. Either Obama is gesturing Hillary is a dog to shoo away, or dog poop to clean off...whatever, the audience understood the insult.