I've seen this in the last 2 or 3 games I've played, and while it never seems to make a difference in the overall outcome, it seems to be happening more and more often.
The AI will sneak a troop transport in, and standard battle will commence, no big deal. They usually ship in 1000 troops VS whatever my planet population is.
What is strange is that RIGHT after that, they will invade again with zero troops and actually succeed in killing another few hundred of my population. Those ninja bastards. Has anyone else ever seen this?