There are a number of more or less implicit references to potentially controversial issues in 'Malcolm' like sex and drugs, but I think these are handled with taste (as I said, they're mostly implicit) and as sort of in-jokes for the keen observer.
I think there should be, as this is about a number of teens growing up in a family, and it would be really strange to pretend they're non-existent.
Even a whitewashed, religiously-inspired series like 7th Heaven dealt with subjects like these, so they're pretty much unavoidable in modern society.
In various episodes of MITM, fun is made of racial issues (which happened with Abe Kenarban on several occasions as in Poker #1 and Baby #2), Stevie's physical handicap (Poker #2 and I guess throughout the series) and defiling Thanksgiving with sex with drunken teenagers and condoms and puking into a turkey could be called 'edgy'.
I'm thinking also of 'Reese's Party' with lots of jokes about Lois' final stage of pregnancy and Hal's would-be sterilization. I think Hal says: 'Lois, leave my balls alone', right?
Then there were other jokes about gays, lesbians, placentas, whores, strippers, inflatable sex dolls, drug abuse and sundry which sometimes involved young children, and a prime example when Lois says to naked Hal: 'Stop playing with yourself' in the Pilot, in front of her young teen and pre-teen children. But I never took issue with those, it's done pretty intelligently and in good spirits.
Rich