More civs in play than specified.

were they minor civs?

Hmmm. I don't know. I don't even think I knew there -were- minor civs. OK, call that one a bad bug report until I prove otherwise.

Wait, by 'minor civs' do you mean the guys you encounter when you land on a planet and have to make a decision about? I mean that I immediately encountered 2 planet-owning spacefaring civilizations, replete with logos, each of whom tried to talk to me (but I had no translator at that point).

Minor civs are those that are not selectable when starting a new game. If you choose only one enemy civ, there will still be other minor civs.
I'm not sure how many it chooses to add in though. Usually its 2 minor civs when I select only 1 enemy.

If it's just a logo of a civ, not the actual picture of an alien, then it's a minor race. there can be tonnes of them in any game. at the beginning you just pick which of the five major races are in your game.

There are, in a normal game, 11 civilizations at the start. Six majors (Terran, Arcean, Altarian, Yor, Drengin, and Torian) and four minors (Alexian, Carnoid, Scottlingas and Kiwalisian). The majors other than Terra and one other of your choice can be removed, but the minors are always present.

If any of those civilizations are destabilized, either through a major race's destabilization efforts, or through poor morale from one source or another, systems can revolt and form new civilizations (to a limit of 30 total civs).

I think the number of minor races also depends on the size of the galaxy...yes, it's the square root of the number of sectors across in the galaxy.

I saw another fun bug today.

All major races in play. I met a minor race (can't remember their name -- the atraxians or something? not one of the major races).

the race info screen indicated that all minor races have been annihilated.

Did you have any screens that came up saying that some people had rebelled?