There have been a couple times when I've been at war with a pesky neighbor. I'd be flying a scout fleet around and accidentally end my turn next to the opponent's rally point. My ships would be ignored and the next turn I'd attack the ships in the rally point till they were all gone

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I haven't seen where this has been reported before, but if my lowly troops are spotted, the opposing fleet should stop waiting for more reinforcements and take advantage of the bonus in attacking first. Even if they die, it's still better odds than waiting to be pummelled into space debris.. In my last occurrance, they had enough sitting in the spot to take out my fleet. But, they never formed a fleet, so after a few turns (and much less damage), they were finally elminated.. (race difficulty set to intelligent).
There doesn't seem to be a problem if they're already in a fleet and 'on the prowl'..