"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 the ship down (unless it pushed the universe up).
After Zoidberg eats the sardines, there are less in the bucket than he ate when he eats the dry stringy night-crawlers.
Zoidberg's underwater house burned down from Bender's lit cigar. When he blows, smoke out of his mouth. However, Bender wouldn't have been ablke to lite a cigar underwater.
Electric eels do not exist in deep waters, so Bender wouldn't have been able to encounter it.
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.