Dont know wheter im stupid or this is actually a bug: I open PKHeX --> Click on "Zygarde Cells"-Button --> Click "Give All" and set the Total from 53 to 100 --> Export the main to my 3DS --> Import it via JKSM in 3DS   Then I open my bag inside Pokemon, switch to Key items, click on the Zygarde Cube and choose the second option it says: "You have collected 53/100 Zygarde-Cells. At the moment you got 100 in your Cube" (Game is German, translation probably not 100%