I am sure that the notation of “he has a wife in the Philippines” is (A) not an immigration clerk mistaking the PI for Hawaii or (B) Stanely Ann.
So that leaves... someone else in the PI.
The obvious answer is (C), Obama Sr. got confused between the PI and Indonesia, and wasn't much interested in his wife, and hence told the immigration clerk incorrect information about the whereabouts of his soon-to-be ex-wife.