I remember in that mission, for each wave of Vagos, I always had to go out and look for the last hidden Vago. There are a lot of houses in that whole area, so maybe there's a crouching Vago behind a house corner or bush, etc.
The best way to find out for sure where that Vago is, is to just walk out till he shoots you. Plus, aren't the Vagos marked as blips on your radar/map? If you're totally sure that there area absolutely no Vagos left, then I guess it's another glitch. Just start over. Imo this mission isn't that hard, so it shouldn't be so bad.