The Xykon character card and move token are counted among the Xykon cards, yes. They're cards that you use when playing with Wandering Xykon, aren't they?
The wandering version of the Creature in the Darkness and the Goblin Zombie were last minute monster additions made after the box was designed. Math is Hard had been cut from the game when it had different text, but was added back in at the last minute with new rules. Thus, there are three more Battle Cards than what's listed on the box.
I have no idea why the rules have the completely wrong numbers, though. I guess nobody checked it.