Sounds sorta similar to a bug I reported in an earlier beta, where a planet culture-flipped to me but there was still an AI ship in orbit.  The developers said that bug had been fixed, but I have been unable to confirm it.

Anyway, yes, this sounds like a bug to me.  You should edit your original post, select "GC3 Support" from the Categories drop-down list in the header, and then submit the edited post to move it to the Support forum where the developers will see it sooner.  It could also be useful if you have a saved game to keep it around in case the developers want to see it.