Long, long ago it did some testing and no matter what you do, the AI can pick which fleet to attack. Build order of the ships, nor creation order of the fleet, nor arrival order in the tile seem to make any difference.
I mentioned this in a dev stream and Paul said "Don't worry about this, the battle dialogs are just place holders. We're going to overhaul the combat interface when the battle viewer comes in, and in the future this should not happen.". And that was either during the alpha or Beta 1.