My husband over stayed in Philippines for 3 years, he has dual citizenship but his Phillipine passport had expired what do we do and how much is the penalty that he needs to pay.
As noted in a comment, expiration of a passport does not constitute loss of citizenship. Your husband might be subject to the same penalty that any Philippine citizen would face after allowing the passport to expire while residing in the country. I do not know whether Philippine law imposes such a penalty, but most countries do not.
Since your husband is a Philippine citizen, it is probably not possible for him to overstay in the Philippines. Immigration law and penalties are generally directed at foreigners, a group usually defined as everyone who does not possess the nationality of the country in question. This excludes dual citizens.
As suggested in another comment, it is possible that Philippine administrative practice would treat your husband as a foreigner if he entered the Philippines with a foreign passport, subjecting him to immigration penalties despite the fact that he is a Philippine citizen, but the countries with which I am familiar do not do this.
The proper course of action for your husband will be to apply for a Philippine passport. There should be no penalty.