I've never had this happen with the SPQR. The only time they get more territory is when I give them territory (and promptly take it back and exterminate to reduce population squalor). There were a few instances where I got one of my cities bribed by a roman army, but it was usually the Brutii.
The way I played it, the Senate faction was destroyed once you took Rome, despite there being plenty of family members (and an heir) outside of the city. This is because the game looks for controlled cities, not existing family members. Anyone left over when the faction is destroyed goes rebel.
But I've never had the Senate survive the capture of Rome in all my games, so this puzzles me.