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You can board enemy flagships.
Disable them in sea battle (cannons/broadsides).
Use grapples (from cannons) to connect and pull them close.
Captain then clicks "Board" crew swings over to other ship and battles crew, and plunders ship should you succeed in defeating all the crew.
(If your talking about a glitch however, I think this ability has been resolved, although there are always new glitchs.)
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