Don’t really know how it all went down.
I would bet the Capt. said he had to go, and then told them “Here, hold this”. So of course they untied him.
A SEAL in the water yells “JUMP” and the Capt. dives in. The pirates poke their heads up to see what is happening, and POP! POP! POP!, goes the weasels.
I thought I saw where the other one may have been injured. Him, being used to the sway and roll of little boats, and not the instability of large ships, probably lost his balance a little and bumped his head.
But this is all just a guess.