Firing your front cannon on the Gargoyle ship, when next to an Ork ship will cause you to Grapeshot your own ship as well, which worse still also sets your own pets onto you and thus gets you killed... GRRR.
Ship repairs should take the resources out of their own hold if the Captain initiates the repairs. Having to keep taking resources out in small amounts is frustrating and ruins a lot of the fun of ship battles.
The Emergency Repair message is a little confusing, and should make quite clear it's not X minutes to finish the repairs, but X minutes of sailing time.
As has been repeated elsewhere, the resources required are insanely expensive to repair for shops, extremely slow and expensive to collect for firing cannon, and prevent any even vaguely effective attempts to solo the content. Gathering together may prevent this, but just means everyone gets ork ships extremely quickly instead as everyone in the party gets the reward roll... but the resources for capturing a ship are so small, no one will bother.
Ship damaging in Trammel should be patched out; already we've got people extorting "Sailing Taxes" on Europa which are more than you'd gain if you went and did the pirates (and you get nothing at all except fish bait from most Fishing quests). Combine that with the above huge resources, and once the idea of griefing trammel catches on with the wider sociopathic audience, it will lead to the abandonment of the seas.
Ship dyes should be named for the colour they are, as some of the colours are too close in the tub to tell what they are before purchase, let alone what they'll become if applied multiple times. Also another bug, applying paint when already at the maximum uses up the paint before giving you the warning you are at said maximum.