I don't play BI, but this seems similar to what happens in R1. If the city was once in the hands of a Roman faction, and that faction is still alive, you will often get a Roman rebellion rather than a rebel one, especially if your culture penalty is high. Sometimes a rebel settlement will revert to it's "originator" or founding faction.

I mean RED WRE romans, not green rebels.
I take it that there are no Brutii in BI? Being an expansion of RTW perhaps some weird glitch had the game dipping into RTW coding?

I was proceding with my usual method "revolt and related annihilation".
There are better ways of dealing with population unrest that virtually eliminate the rebellion problem.....