@j-r-c
It could be actual Indian DNA for those who are 6-10% range but in the case of most Pinoys who have only 5% or less South Asian/Indian, its more likely it is something Negrito or some type of "Australoid" Ancient Ancestral South Indian blood than actually South Asian gene flow.
Meanwhile most other SE Asians can easily have up to 15-20% or more Indian/South Asian blood. I have also seen a few Burmese, Thai and even Malaysian DNA results who score up to 30-35% Indian ancestry.
I'm not sure. 3% sounds pretty low to me. Those Pinoys should upload their results to Gedmatch or other DNA tests like Global25 by Davidski, to see whether their South Asian will increase drastically or not. If its remain the same 3% in Gedmatch, it might be something Negrito-like.
Another way to tell is to see if those Filos score any Baloch component in HarappaWorld along with S_Indian component, if they have both, its likely their South Asian is legit.