1. Why shouldn't "None of the fish in the aquarium IS native" be "None of the fish in the aquarium ARE native?"
Take out all of the prepositional phrases in the sentence (the test writers try to hide errors by stuffing the sentence full of prepositional/other phrases):
"None are native."
None is just short for "No one." Does it make sense to say that "No one are native" ?
2. Why is "The civil engineers who designed the city's streets in the 1800s could NEVER HAVE FORESEEN" better than "The civil engineers who designed the city's streets in the 1800s could HAVE NEVER FORESEEN?"
Neither choice is "better" than the other (and I doubt that both of these were answer choices). You probably thought, "Oh, this sentence can be better worded this way." Remember: just because you can think of a different wording for a sentence doesn't make that sentence grammatically incorrect.