Remember near the end of the third episode they found a survivor from the sunken ship. Adam Kadyrov manages to slip past the policeman at the hospital dressed as a janitor. He asks the survivor what happened on the ship.The guy tells Adam how the captain starts killing some of the passengers because he isn't getting enough money out of it. Now here's the solution ( i think ) - The survivor sees it all happening from the bridge because he is the helmsman, he's steering the ship. He gets so overwhelmed and shocked by seeing his captain shooting the illegal refugees that he fears for his own life, leaves the bridge and probably jumps off-board ( this isn't actually shown, i'm just guessing that part ), leaving the ship astray, whereas it probably hits something and sinks.