It was Captain Jaggery who killed Mr. Hollybrass, his first mate and most loyal crew member, over an argument concerning sailing through a storm.
When the hurricane was about to hit, Charlotte heard Jaggery and Hollybrass arguing heavily over what to do. CPT Jaggery wanted to sail through because it would look good in his book, and would enhance his already blown-up ego. Hollybrass thought that this was a stupid decision. The problem is that the issue escalated to the point of murder. This was also a great opportunity to get Charlotte involved, since Captain Jaggery really began to detest her, so this is exactly what he did.