Maybe they were at a lower level than you were when they fought him. Some people skip side quests and without the xp, don't level as fast. Perhaps you made better choices when you picked talents and abilities for your crew. Maybe they were not as lucky with their gear drops or aren't wearing clothes that best enhance their type of pirate. Some captains make better use of their crews and learn fast how to best use their talents. If they didn't train a heal from the Commodore, don't wear any gear with a heal, and don't use Bonnie to heal for them it could be hard too. There are so many reasons it could be.