"It is not a port, it is a farm."
Translation:To nie jest port, to jest farma.
Let's focus just on the second part: "It is a farm". You cannot use Instrumental in such a sentence. It would be as treating "it" as some kind of a noun, but it's a dummy pronoun. It's a "This is Y" sentence and such sentences use Nominative. Same applies to the first clause, it's just negated.
More info here: https://www.duolingo.com/comment/16373167