For example, it points out the butterfly toys with the idea of it being related to the storm... but then doesn't notice that the Butterfly's main two appearances are to herald Chloe's first and last appearances in the story (which is a clear link). the argument for Chloe's survival not being the cause of the storm is based on the death in Episode 4- forgetting that the damage to the time line has been done by that stage (which is why the storm still happens- it's too late to "course correct"). One of the main uses of the butterfly in the game is that very obvious butterfly effect- Chloe is the butterfly who'll flap her wings and cause a storm. To stop the storm, stop her flapping those wings. By episode 4, she's already flapped those wings, squashing her now does no good.

This has also been confirmed by Dontnod (as has the doe being, essentially Rachel's ghost)

This is a very "not a time travel story" reading of the story, and so it misses a lot of very obvious stuff due to it being a time travel story.