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Well, this actually came up on the first episode when Loki was debating with Mobius. It was explained by Mobius that this was supposed to happen on the sacred timeline which is why the TVA didn't do anything about it. My guess is that the nexus where past Thanos came from didn't diverge enough to cause damage to the sacred timeline. But then, how did Loki know about the Avengers going back in time trying to collect the infinity stones when it hasn't even happened yet on his point in time. I wouldn't know much since I'm still up to episode 2.