>The document lists Barry Soetoro as a Indonesian citizen
That doesn't mean he's not an American citizen. A minor child can't renounce US citizenship, nor can a parent renounce it for him/her.
If he was born in the US, or born out of wedlock outside the US, he would get US citizenship from his US mother (assuming 1961 birth date is correct) according to US citizenship law and no other country can take that away. It would have been up to him to decide at 18, if he had a second citizenship that didn't allow dual citizenship, which one he wanted to keep and renounce the other.
Indonesia, in this case, can't determine US citizenship law. No dual citizenship arguments go awry because they don't consider that no dual citizenship cases apply to a citizen from a no dual citizenship country that takes on another citizenship. If an Indonesian, for example, took on a US citizenship, Indonesia requires that they denounce Indonesian citizenship. The US doesn't have a dual citizenship law.