Yes, this one drove me a little nuts when I first started seeing it in my games because I wasn't sure what I did... As stated above, that will do it. I also found that if you have an open borders treaty with someone and then ask them to remove their ships from your territory (I did this because they were parking massive amounts of ships around my planets/starbases/shipyards) will also do it. Probably some other things that I haven't noticed or figured out yet, too. I actuially started a thread on this very topic a couple of months ago. Do a search to see if any other relative info is to be had there.

I did search but found nothing on the subject. 

Still conflicting information around. I will try the different thing suggested to see if I get it in a skirmish/sandbox game instead of the campaign.

This penalty seems to always happen when I invade minors. 

I saw it in one of my sandbox games.  Seems similar to the "we know what you're up to" from GC II when the AI was suggesting that you were about to invade its territory and/or mess it up.

Here in GC III I suspect it has something to do with declaring war whilst you have a treaty/trade with the AI faction.  Or possibly declaring war when you are within the borders of another faction sneak attack style.

Or not.  Only really noticed it once after the fact after I DoWed someone and was in the process of cleaning their clock.