"The Pokémon Company is [Nintendo's] affiliated company, accounted for by using the equity method," states the letter. "Because of this accounting scheme, the income reflected on [Nintendo's] consolidated business results is limited."
Monday was the first trading day following the letter, and Nintendo stock fell 17.7 percent in Tokyo, which was the company's biggest fall since 1990, according to Bloomberg. That's $6.7 billion in market value. However, the company's value is still up overall since the launch of Pokémon Go. Bloomberg says that most investors knew that Nintendo wasn't the publisher or owner of the game, and Nintendo wasn't trying to make it appear as though they were. Nonetheless, the letter, which states that they aren't revising their financial forecast upward, may have cooled people on the stock. Couple that with some short sells and a fall harder than entering your local gym with a Magikarp is the result.