Unfortunately, I don't have any screenshots of this bug to help, but I was playing a single-player game last night with Occupation victory enabled, just to see what it's like.  First, I kinda like it, but the AI never went after the planet (which was a disappointment considering all the defenses I put up there), allowing for a very easy win.

However, my problem comes in with the neutral AI guarding the planet.  The name of that group in question was "Eta Sector Remnants".  Not entirely sure if that's constant, as I've only played one game with occupation on, but anyway.  I was playing the game as TEC Rebels with the Truce Among Rogues tech researched.  The AI controlling the planet was still hostile, which I'm assuming was intentional.  However, when I went out to another galaxy (with no players occupying the system) after claiming the occupation planet, other neutral factions named "Eta Sector Remnants" remained hostile despite them both being TEC as well as having the TAR tech researched.

I think what you guys did, without seeing the code, is have Eta Sector Remnants set as an exception, which is fine and good.  However, other neutral minor AI's are still named Eta Sector Remnants, perhaps unintentionally.  I think creating a new class for the occupation fleet or removing Eta Sector Remnants from the names normally cycled would fix the issue.