Their first clue that it would end badly should have been the fact that the people in the settlement pretty much just let them walk off with the cows and load them on the ship.
Now, I don't know who's been on tall ships, but even the really big ones are fairly cramped. So that was a lot of cow poop in a very small area. And what could the pirates do, I mean.
This one particular Navy captain, who's name escapes me at the moment, was after this particular ship. And when he closed in on them the smell from the pirate ship was apparently so bad.