On June 6, 1988, Donald Wildmon, head of the American Family Association (AFA), alleged that "The Littlest Tramp" depicted cocaine use, instigating a media frenzy. Concerning Bakshi's involvement with Mighty Mouse: The New Adventures, the AFA claimed that CBS "intentionally hired a known pornographer to do a cartoon for children, and then allowed him to insert a scene in which the cartoon hero is shown sniffing cocaine." Bakshi responded, "You could pick a still out of Lady and the Tramp (1955) and get the same impression. Fritz the Cat (1972) wasn't pornography. It was social commentary. This all smacks of burning books and the Third Reich. It smacks of McCarthyism. I'm not going to get into who sniffs what. This is lunacy!" On CBS's order, Klein removed the sequence from the master broadcast footage. Wildmon claimed that the edits were "a de facto admission that, indeed, Mighty Mouse was snorting cocaine". Bakshi agreed to the removal of the offending 3½ seconds from future airings of the episode because of his concern that the controversy might lead children to believe that what Wildmon was saying was true. Wildmon's group then demanded the removal of Bakshi, but, on July 25, 1988, CBS released a statement in support of him.
Editor Tom Klein expressed concern that a sequence showing Mighty Mouse sniffing the remains of a crushed flower resembled cocaine use. Ralph Bakshi did not initially view the footage; he believed that Klein was overreacting, but agreed to let him cut the scene. John Kricfalusi expressed disbelief over the cut, insisting that the action was harmless and that the sequence should be restored. Following Kricfalusi's advice, Bakshi told Klein to restore the scene, which had been approved by network executives and the CBS standards and practices department.
Big Murray was drawn to resemble Kirk Douglas.