What signs show this pokemon as hacked?

[Nemisis]

I have racked my brain on the legality of this Pokemon, all of it's data appears legit to me so I am not sure why it keeps coming up as a problem

[xfr]

Fateful encounter is your problem.

[Ampitere]

Try taking off shiny, because it can cause problems. Just as well, the fact that you have almost all IVs maxed and a crazy amount of PP ups used could also be affecting it. The level met should be 40 because that's what it is when you activate it's encounter.

Here's what I came up with after fixing a few of the potential problems: http://up.ht/maI6Y1

Please let me know if it works, I suggest adding one thing at a time to make sure you're not flagging it as you go. Start with trying to make it shiny because I guarantee that's going to be the most difficult thing to accomplish.