I don't know which exact incident you are referring to. But as far as I know, bowing is a common gesture of respect in many cultures, just like the handshake is for us. I believe in Japan, you usually bow down when you meet someone. So if you're talking about the mere gesture of bowing, I don't see anything wrong with it, on the contrary.
If, for example, Obama bowed down when meeting a Japanese official, that's just a nice gesture that means: "See, I know your customs." Denying it is a bit petty, much like a Japanese denying a handshake when meeting a Westener, just because "physically touching someone means losing the face" or something like that.
But if Obama sold out American interests to some foreign leader who doesn't deserve it, that would be something different, IMO. No matter if he physically bowed or not.