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Those would be bugs and best to report in the bug report thread to help get resolved. Thanks for reporting.
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Tenraix,
I have been working a lot of this out recently, too. I think I can help you here.
What I discovered is that you have to drag the action (the attack roll icon) onto the target ship (either in combat tracker or on a map), and then it behaves as you expect, with the attack roll directed to the target ship and evaluated. If successful, it adds an item in the ship combat tracker to assign the damage to a quadrant or cause system glitches as appropriate.
There may be two ways of thinking about this: 1) the action is really tied to the character and not the ship and 2) multiple gunners can potentially attack different enemy ships, so you need to be attack-specific in your targeting.
Hope this works for you.
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Both issues were fixed in the latest update. Thank you to dev!