Thank you so much @joebloggs, I already had the ILR when i applied for her visa. her visa is valid for 3 years and 4 months, the same year that her passport will expire but not the same month (Visa valid from 15/04/2010 and valid till 21/08/2013. If the visa they issued was meant to be settlement then it should only be valid for 2 years, if i am not mistaken.
I have called the UKBA on the same number 4 times and spoken to 4 different person, the first 3 has said that she definitely has to apply for ILR and the last one i had spoken to has said if I think that the UK Embassy in the Philippines has made a mistake in her visa then i should contact them which i already did by sending them an email.
<<<sigh>>> after all what we've been through, her visa refusal initially, appeal process, took more or less, couple of thousands already spent and now after nearly two years, this will happen.