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In one of my friend safari's I've seen all three pokemon, but where it show what pokemon appear in the safari when you select it, it only shows two of the three pokemon.
It's a bug-type safari and the Pokemon are Combee, Illumise, and Vivillon. When I select that safari, where it shows the Pokemon that appear, it shows Combee and Illumise, but not Vivillon, even though I've seen all three.