Vanya is an easy target for fan theories, having been a family nuisance all her life and then single-handedly ending the world in season one. There's a growing body of thought, which you can explore on the show's fandom site, that she was also responsible for Ben's death. This theory agrees that Ben was killed in action, but instead of a death by unavoidable killing at the hands of a foe, they assert that Ben sacrificed himself to save Vanya, whose then-believed lack of powers made her a dangerous liability.
Ben never wanted to be a hero and often lost control of his tentacle powers, so it's not far-fetched that he got carried away while trying to save Vanya, ultimately costing his life. The theorist claims a scene in the third episode of the first season provides evidence for this when Diego tells Vanya to stay out of the way of a mission, giving her a look like this warning has good reason.