Xenophobic synthetic scavengers. You get that early flat +1-per-resource mining boost, so all you really need is one or two sources of durantium and promethium each and you end up more-or-less unstoppable.
Having the same problem here, used the turn cheat to bypass the lost citizen prompt, but there's still the issue of the unselectable citizen ship just sitting in place taking up a space. The "destroy" command doesn't work without it being selectable, or providing an object ID, so...
In my experience, it can often be explained by looking at the motivators in the Diplomacy window. "You are out of our reach" or however it goes is typically the reason - they're pissed off enough at you to declare war (if you're avoiding building up a military at the start, this'll easily cause early declarations of war), but they don't bother to check if they can actually send warships out your way before declaring war. Then it's "oh... right... nevermind."