I cannnot system, because enemy fleet guards it. Though i cant attack this fleet because it says it cannot participate in battle.

How do i invade them? Or is this a bug?

I have the exact same problem and I don't know why ! It's frustating, I'm trying not to win any other type of victory than supremacy and conquest because that's what I'm aiming for but I cannot even invade the enemy main system... There's a civilian ship and it's written that it's a pirate (?? )... I don't know what that ship is (this game is sometimes unclear...) but it is invading the system and as it does, I cannot attack it or invade the planet...

What if the ship belongs to your ally, but disguised as a pirate ship?