Mark, I hope your son has not overstayed....... If he travelled on his British passport and cannot show his Philippine passport, he is still liable to overstay if his visa has expired.

We had a similar problem when traveling to China as a family, as we only showed my children's UK passport, it looked like they were overstayers even though they had never been anywhere else. Once we showed their Philippine passports the problem was solved as they are duel nationalities.