Your wife's passport must be valid upon application of ILR. Renewing the Philippine passport would take 5-6 weeks.I guess the best thing to do at the moment is to call UKVI so you'd be guided properly on what to do.
Also, you can read these links. They have the same situation with your wife, although they failed to mention whether their application was successful or not.
http://www.immigrationboards.com/ind...lr-t96349.html
http://www.immigrationboards.com/ind...e-t102818.html