Not sure what you mean in your first question. Do you mean that the crew doesn't target anything? If so, you either have to lock onto a target with the binoculars, by lining them up on the target, and pressing the spacebar, or go to the deckgun menu via the icon to the lower left, and click on automatic targeting. Same goes for the AA gun, via its icon. Also if the target is out of range, they won't fire on it. Remember, the deck gun, and AA gun(s) are short range gear. Gotta be up close and personal to shoot at stuff.
As for the crew not clearing the bridge, TMO usually doesn't have that issue, as it was a stock bug that got sorted out long ago. Although, it could happen still if you ALT + TAB out of the game. Also, if you do ALT + TAB out of the game submerged, it can cause the game to not recognize when you surface, to clear the CO2, and the only way to solve it, is to save the game, exit out, and restart the game, and don't ALT + TAB out of the game unless you have to.
Hope this helps!
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A legislative act contrary to the Constitution is not law.
-John Marshall Chief Justice of the Supreme Court
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