The show centered on a so-called "buried secret" that the Los Angeles Times says did not exist.
The scheme was a "guerrilla marketing campaign" that went too far, admitted Bonnie Hammer, network president.
The Times said the network had hoped to promote their documentary, as well as Shyamalan's upcoming film, "The Village," by announcing the filmmaker had stopped cooperating with the network after the documentary's questions became too personal.
"This marketing strategy is not consistent with our policy at NBC," said Rebecca Marks, NBC Entertainment spokeswoman.
NBC Universal recently took over Sci Fi, which is available in 83 million homes.