I recently received a shiny Darkrai lv 100 in a premier ball. I tested it out on GTS it said it's a special Pokemon, yet I put it in the Pokemon Bank to trade between X and Y and it did so.
I am confused please help.
Special Pokemon, are Pokemon received via events so that's y you weren't able to deposit into GTS as event Pokemon aren't allowed. So the darkrai can be a legit one. It's actually difficult to check it's legitimacy but if it's 6IV it's almost certainly hacked.
Hope I helped :)