Hey guys, sorry it took me so long to respond to this.
There is a limit of 100 factions currently set in the game. Their is a limited amount of shader registers, if we went higher we would need to buffer some of this data, which would mean more memory is required. Not that it isn't doable, we may look at increasing that cap at a later date. I talked to the team a bit about increasing that limit to 128, but we will need to QA that and make sure it works before we release it without knowing the full memory implications.
I certainly agree that the game shouldn't allow you to put in more than the total allowed factions and then crash. I'll get a bug in to not allow you to add more than 100 total factions (and if you fill all the slots them minors will not be placed).
As for minor's vs major factions. Keep in mind that except for a few limited differences (most notably being able to build colony ships) they are the same thing. From the games perspective there is little difference, so they definitely take up a full player slot. I am sorry if we were confusing about messaging 100 major factions plus minors. You could mod a game with 90 minor factions if you wanted.
Please let me know if you have more questions.