The one that stuck out for me was 'Naomi in the ship' where they never made it clear that the ship was disabled/a trap and it seemed the entire episode was her wandering around and emoting. If you knew what she was doing - by reading the book - it was ok, but anyone just watching the tv must have been very confused. All it needed was her to mutter a few words to herself .. meh.
i thought it was pretty obvious the ship was a trap. the dude was wiring explosives up prior to leaving her on it. and they made it pretty clear by talking about the plan that they were using her to lure the rocci there.