Your message suggests there is both a possibility that he is a US citizen and also claims that he is not a US citizen.

If it was 100% clear that he is not a US citizen then I don't think they would have let him back into the country. I'm curious to see how they are going to prove that he was not born in the US, assuming his US birth certificate is valid. Ideally the Mexican birth certificate shouldn't take precedence over the US one.