Ya, I just reported it the other day. I couldn't figure out what was causing it. One of my custom sovs leading Resoln was the one being replaced by Altar (led by Marken in my case), but there was nothing I could find wrong with that custom sov and I could play as them just fine. I had also played against them several times before without issue.

This happened all of the sudden two games in a row, I just ended up deleting that sov more because my list was getting too long but I haven't seen it happen since.

Just met an Altar led by the Oracle. This is getting annoying.

I can't remember the exact situation the last time this happened (have to look through all my saves), but now, they were both Altarian red, so I cannot tell the difference between them on the map. Again, it breaks immersion (important for a game where RPG is a strong element!) and it now even hinders gameplay.

I do not agree with the post above that this is an acceptable solution: I'd much rather have it so that it's not possible at all, using default opponent settings, that twin factions exist on the same map. It's no coincidence that Civ also doesn't allow this in the default settings. If the player wants to mix and match, do it as an optional setting. The player's free to do so if he's not bothered by this.But now, there is no way for me to do this, except by manually picking opponents (which is not what I want to do!)

Perhaps it even alters game balance, as a sov with faction A strengths can be overpowered if he's actually leading faction B. Not enough experience with this by a long shot yet to comment, but with Civ4, mixing rulers and civs could lead to some absurdly overpowered settings.

I really wish this to be fixed. It's obvious when it happens, it's easy to avoid if your opponent-selection algorithm picks factions first and sovereigns second. And make mix-and-match optional.