(My knowledge in Filipino os bad, so perhaps I didn't understood something you wrote.)
That's a problem if having money belonging to other on wrong person's acount, because in juridical point of view TOWARDS THE BANK these money belong to you even if they don't in other point of view.
I suppouse the bank deduct money from your acount of some reason e g for a not paid dept. Dept to the bank, dept to someone else or what?
If to someone else - has a court (including baranggay "court") decided the bank to do such deduction?
Or have you done some other agreement by which the other party get right to deduct money from your acount?
If it isn't a dept to the bank, you haven't made any such deal, and no court have decided the deduction, then you can go to court to stop the deductions.
If you are LUCKY it's some chance the court can include in the desision some of the money on your acount isn't your's. Do you have some deal document showing some of the money isn't yours? Or some other proof/indicium some of the money isn't yours ? Courts like documents, it's common they bother much more about them than what's just told vocaly to them.