"The dark matter engines don't move the ship, but instead move the universe, allowing the ship to go faster than the speed of light" Was the explanation given by Cubert of the engines in the Deep South but the giant Bass was able to pull down the ship (unless it pushed the Universe up)
Zoidberg's own underwater house had Burned, Bender burned it with a Litten Cigar, When He blows smoke out of his mouth, Smoke came out of his mouth, However, Litten Cigars & Smoke Doesn't Exist in Water. (I'm not sure this is a goof. Hermes is quite clear about the improbability of that situation.)
Hermes uses sardines as bait even though in A Fishful of Dollars sardines are confirmed as extinct and Zoidberg eats the last existing ones.
Electric eels do not exist in deep waters. So Bender could not have got shocked by the electric eel for one scene.
One exception is if electric eels changed their habitat over a course of 1,000 years.
Another exception is that the electric eel escaped from somewhere or was released into the wrong place.