A few weeks ago, I completed all the main quests/contracts for the Dark Brotherhood. The one where you have to kill the ship captain was really strange for me. I snuck onto the ship at about 2 AM and when I entered the ship, in sneak mode of course, there's a bunch of her crew sitting right there at a table staring at me, Safia among them. So much for sneaking . . .

I go into attack mode, killing her rather easily and her crew attacked. I killed most of them, although had to dodge and run a whole lot until I didn't see anyone else coming for me, then went back to the Sanctuary. Was there a better time to go onboard the ship? Job done, but I hated not having it be a clean job. Too late to do anything about it for this character, but I'd still like to know if I did something "wrong" and if there's a cleaner way to pull this job off.

Some of the crew are essential and cant be killed.
Usualy the crew on seeing you, will inform you that your not welcome and should leave but they never attack you and just get on with whatever they are doing.
When you get to the Captain you have the option to tell her the brotherhood sent you, On hearing this she will then initiate an attack on you, You can then kill her eaily in self defence.
The crew will not help her or attack you, some will say things like, its not my fight or Im staying out of it. But beware of accidently hitting any of the crew though, as they will all attack.
When i did the contract Sofia was stood behind a crewmate and i couldnt get at her to swing my sword to kill her and had to get her to chase me out of the room to a less crowded area away from the others.
Once she is dead, loot her body and return to the sanctuery.

Weird. I just did this quest and found it surprisingly easy. Why did they make some of her crew essential if they are going to attack you? When I entered, the crew was right there by the door, but Safia was downstairs by herself. So I snuck up and killed her easily, but then on the way out I thought I'd sneak attack the crew members too, only to find that the one I attacked was invincible. Lame.

There was something like a party going on in Sofia's cabin when i was there thats why i had to get her in the gangway to kill her.
Maybe the 'essential' sailor was so someone was left to grass you up to the guards if you went postal.

Sounds like I could have had an easier kill, but I just freaked out when all the crew was RIGHT THERE staring at me.

Stage fright?