I have been starting conventional new games and at least half the time I get aliens in my starting system. Not just ships showing up, but owning a planet. Is there a setting to prevent aliens from living on the planet next door?
Are you playing real stars or custom?
Do you generate a new system or starting from Sol?
Did you flag the race starting in same system when setting up the game at the start?
From my experience I never had another race/spoiler/alien in my starting system unless I set it up that way and I don't even know if it is possible though. And we talking about hundreds of starts in VB6 and probably almost 30/40 on C# if we consider all the patches/bugs that forced me to restart a campaign.