IIRC:
1. To remove the child from the parents US passport having nothing to do with nationality of the child.
2. Because the child has obtained his own new US passport (based on the report of an HI birth by the grandparents...real or fraudulent), possibly to enable travel with another adult, not the parent...also having nothing to do with nationality.
3. Obtained a passport from another nation.
Removing is not proof of anything in terms of citizenship. I believe that is your primary point. Yes?
Since he was apparently removed. What passport did he get? A US passport or an Indonesian passport? Or British or Kenyan? (Just to cover all the potential bases!).
Knowing this would put to bed a lot of not-so-enjoyable speculation.