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I went into your safari w/ a Trace ability and found all three pokés with HA. Perhaps you are getting unlucky. Marvel Scale Dragonair (it doesn't have Multiscale) is what you should be looking for.

Three is the maximum amount of pokés any safari can have. I've had about four to five people tell me that my safari contains Fraxure, Dragonair, and Sliggoo. What species are you seeing (3 pokés)?

I have defeated the Elite Four. I am pretty sure the third pokémon is Sliggoo, which if I am not mistaken, is the only pokémon that would be affected by whether or not I have beaten the Elite Four (In other words, Dragonair would not be affected).