These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Mis-blamed: The Forerunner Saga is often pointed to as the 343 Industries canon source that changed Forerunners from ancient advanced humans to a separate species. The Forerunners and humans being separate species was actually established in the terminals of Halo 3, by Bungie themselves.
Another common complaint is that the series turns the Forerunners and Flood into hyper-advanced species with mindbogglingly-advanced technology. Ignoring the fact that the first thing we've seen in the series is the ten-thousand kilometer-wide artificial world with a weapon designed to destroy all life in the galaxy, and the Flood are so terrible that such a weapon is needed to defeat them....
Moral Event Horizon: The Master Builder crosses it when he uses a Halo to punish the San 'Shyuum for rebelling. Even his closest allies thought he crossed it.