In fact, it is not even a different mechanic for the AI. It is simply that you need to be there to fire those guns manually and you are not when you end your turn.
The best way to prevent such a situation is to have a defensive ship of your own patrolling the system. The AI plain suck very big time in Ascendancy so it is more than easy to design a ship which can destroy anything in its path.
Another option would be to pass your tactical turn. I think there is an option to do that in the planetary system menu. This would take the opponent ship into range before they land to your planet and you'll get a chance to hit it.
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