You're connecting real world intelligence with anime intelligence. It took so long for konoha to figure out they were revived corpses. Even someone like shikamaru who figured out hidan's jutsu couldnt figure it out instantly. Jiraiya did take a considerable amount of time to figure it out. In anime world, chibaku tensei, isnt easy to figure out, otherwise naruto wouldnt have panicked that much. To us viewers, it was obvious, pain were corpses with fake rinnegan, but for jiraiya, it was such a complex tiddle to crack, like who the hell has six people with rinnegan, a pair of rinnegan itself were considered a myth at that time, still jiraiya couldnt use common sense, since it is anime world logic. Rest of it has to do with battle intelligence and analytical abilities.
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