Fragment, but why?

Don't know why Kjk but here's how I would have punctuated

Then instead of making the "Magic Creatures vs Nazis" movie you have written, consider making the magical side far weaker, giving a greater sense of impossible odds and making the movie more appealing.

Though I still don't quite understand it

Try eliminating the word then. It's possible that the program (which is an imperfect grammar checker at the best of times) thinks it's a dependent clause.