^ Well, I know what you were referring to, but it's a chicken-and-the-egg thing: Was the instruction book not changed to match the box... or vice versa?
Besides, there's plenty of games that have different art on their instruction book than cover, like SM64 and SMS (although I'd just like to say "idiot" to whoever commisioned the design for the majority of N64 instruction books. "The logo on an orange background? Here's a raise!")