So I just finished the Winning 2 Intermediate puzzle by attacking Feld and capturing the enemy queen. It was not a Neptunium victory. It states that I won the game in less than 48 hours but it also says that I have not yet finished the puzzle. What else can I do?

Win the game by getting 200 Neptunium.

That's an interesting way to "beat" that puzzle, haha. But it's not the canonical solution.