That explanation is in the linked story. Scroll up, click the link, read it. My hunch is that the arresting officer misunderstood the fellows broken English. The judge involved clearly understood the fellow was a citizen when presented with his birth certificate, but had to follow the ICE holding order. ICE agent arrived, reviewed the case, and released him.
I'm sure it was a very unpleasant experience, I'd be mad as a wet hen if it happened to me, but these things do happen. In the end he was unharmed and released.