I can only discount that it was not a counter attack.
For marauders, would they have marauders in their name? We did not have any minor factions turned on if it was one of that.
We have it happen now and then, enemies will pop in one by one all over the sector, we have never been able to nail down what causes it.
I thought one way to prevent it was to have a large force in that system, but in the example listed, i had about 700 ships, but based on the ships the enemies were using I had very poor bomber research which led to the ai fortress taking awhile. The whole time enemies would just appear one by one all over the place.
Also, don't suppose there are any quick ways to select portions of a group? Right now I've only found to cut a group in half is to ball it up and drag a box over half. Works well, but when you want to split into 3rds takes a bit more.
I find I constantly am splitting groups to make them smaller for low range units. And since I like all the ships that give bonuses to friends around it I pretty much always do group move instead of just letting them run off to get into fire range.