Inefficient Planetary Administration Influence Modifier
Solution 1:
It is because of having too many core planets. A planet which is in the colonization process (i.e. where you still pay 8 energy upkeep and cannot build yet) also counts towards the core limit, even if it isn't shown.
If you colonize a world while at your core planet limit and then add it to a sector it will usually stay your core world until the process is completed and incur the penalty.
I've also had a bug, where such a world incurred the penalty indefinetely and I had to remove and add it to the sector again to get rid of it.
So, if possible add a system to a sector before colonizing it, if not removing and readding the planet to the sector should fix it immediately.