Not really a plot hole, plot holes are when two events in a story contradict each other. The best explanation I can come up with is underestimation. Sure they have fought us and challenged us before, but keep in mind we were always leveling up, getting stronger and unlocking new abilities. I don't know about you, but I reached level 20 mid mission, right before the boss. They were still learning about what we could do.
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A plot hole is any inconsistency in storytelling. It doesn't need to be a conflict between two events.
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Probably thinking of discrepancy, close enough lol