Please be more specific in your question.
Your brother is in Phil after a long stay..How long?
His Filipino passport expired..While he was in Phils?
What passport did he use to enter the Phils
Is he a dual citizen?
Did he show both passports on entry?
Be more specific and I will post my thoughts.
A Filipino passport can be renewed in Phils inexpensively
Just takes a bit of patience and a bit of a wait
Incidentally I was travelling out with my wife who is a dual citizen.Her Filipino passport had expired and she was using her British passport. She was stamped out,then the Immigration officer asked for her Filipino passport,realised it was expired and cancelled the exit stamp. She was told she was an overstayer for 7 years and there would be a very large fine to pay.
The problem was resolved after a chat with the supervisor
The issue of your brother may be similar. Please update the info