This has been happening to me pretty consistently - I'll get a message from an AI about something, and when I hover over their disposition, the message "Your civilian ships have trespassed in our sovereign space" is displayed there along with others such as "You weren't hostile towards us," etc. First I noticed this when I just hadn't been in their territory - I figured, eh, maybe some trade vessels went through their territory or something? Now, as I've played more games, I'm consistently seeing this message even when I'm only a few turns into the game. I don't even know where they are. The only color on the map is mine - and when I do find them, they're pretty far away from me. 

I'd be happy to supply a save game or two (if you can tell me where they are located in steam files) and I can most likely replicate this with ease. I should also note that I updated with the most recent hotfix and the pictures attached are from a brand new save game.

One other thing I'd like to mention, while I'm here, is how ridiculously protective the AI are of their borders. I can usually get away with explorer-type ships and neutral vessels such as Vineships, but if one measly military unit sticks a toe in their pond, seconds later, the AI get very upset. Two more turns and it's from peace back to cold war and an air of extreme disappointment. It makes doing the Academy quests - or any quest that involves going somewhere, with military units, that is not inside your own territory - very much impossible. And not only do they get upset about their borders, but they will parade around their ships inside your borders and you have no option to express your disapproval at all. 

Here's pictures from my current game