They said Ragna just magically got an arm out of nowhere. He got it by attaching the Black Beast's corpse to it. That's right in the game itself. They were using the anime for some reason for that part while they were using the game for some other parts.
Then there was the whole explanation about the church scene and some other stuff. They could have at least gave a cursory explanation about something like the Power of Order but they just twisted things to make it sound dumb for a laugh. There's plenty of stuff only in supplementary material only, but as of Chrono Phantasma there's a decent explanation for pretty much everything that the video actually covers. Like time travel -- obviously different stories treat time travel differently: some of them have a loop where the past influences the future, others create alternate timelines, etc. So there was no reason to just make it sound like the story was just being stupid because of their misunderstanding.
Well, it's not a surprise since that's their basic schtick anyway.