In the musical segment for "Down in the Valley" has Theodore giving the audience the finger during the line "hear the wind blowing, hear the wind blow."
In another musical segment, "Oh Gondeliero!" has people seen drinking alcohol.
In "Bicycle Built for Two", Dave (a grown man) gives Daisy Belle (a girl) a bike ride all the while singing to hernote he gives her a ride because the Chipmunks were distracting her so they can take turns riding her new bike... after she told them that they couldn't ride it!. If it were present time, Dave would have been considered a phedophile.
In "Romancing Miss Stone", during the scene where Alvin and Dave are duelling over the hand of Alvin's teacher, Alvin yells out "Take that, you gigolo!" as he hurls a water balloon at Dave.
In the infamous "Sploosh" episode, Brittany's character at one point asks Jeanette (as the mermaid), "Are mermen sexier than human men?"
Even better from "Simon Seville, Superstar", Simon (an eight-year-old boy chipmunk) is asked how he feels about being a SEX SYMBOL! He is unsure how to answer that directly, but suggests that his glasses may have sex appeal.
In "Cinderella? Cinderella!", where Brittany dreams herself in the role of Cinderella, a scene of her forced to do various chores has her giving baths to her sisters. Both Jeanette and Eleanor's expies in the dream are shown sitting in small bathtubs, uncovered from the waist up, with small dots drawn on. Admittedly, such a thing back in the 80s was probably no big deal unlike today, but come on, what the hell?
Also, depending on what The Chipettes are wearing, it seems like the animators like to draw them with busts from time to time, despite them being eight-years-old. Most notably, in the episode "Staying Afloat", bikini-clad Brittany constantly goes back and forth between being flat-chested, and having breasts.
"Dreamlighting", which parodied the show Moonlighting, has what appears to be a distraught Alvin suffering a hangover. Then we see that he's just been drinking root beer and he's had far too much.
In general there seem to be a lot of Panty Shots (from the Chipettes and other young girls) for no reason, although that may be an attempt at realism, as some of their skirts are quite short. Still...
Depending on how you interpret it, in an early episode of the '80s series, Alvin runs for school president, and at one point, his campaign slogan is: "Don't be a donkey, vote for Alvin!"
Alvin sees a psychiatrist in the episode "Alvin and the Analyst", who supposedly is a caricature/parody of a real-life sex therapist; granted, Alvin wasn't seeing the shrink for those kinds of problems, but still parodying a sex therapist on a kids' show?
The entire "Proud Mary" number from the episode "Goin' Down to Dixie" so much that it actually spawned an entire article based on a troll's YouTube comment that The Chipettes are, "A pedophilic rape waiting to happen", on the grounds that their New Orleans-inspired dresses were inappropriate for girls their age, while others argued that not only did the dresses fit the number they were performing, but they're chipmunks, not little human girls. In short, The Chipettes' performance of "Proud Mary" is almost as controversial today as their "Gettin' Lucky" number from The Chipmunk Adventure had become.
The scene where the Chipettes have to get past a swarm of snakes. How do they do that? By charming them, of course. How do they charm them? By singing. (While wearing Belly Dancer outfits, too) And the name of the song they sing? "Getting Lucky". No more need be said.
And the snakes go rigid when they're actually charmed. Blatant Visual Innuendo, much?
The two main villains are seen smoking or at least holding cigars throughout the film.
While The Chipmunks and Chipettes struggle with controlling their balloons, Klaus can be heard muttering, "Gott it himmel!", which is German for, "God in Heaven!", of which can be interpreted as a swear against God, which is usually unheard of in children's entertainment.
Then in Little Alvin and the Mini-Munks, Dave drops toddler-aged Chipmunks and Chipettes (all six are puppets) with his friend Lalu so he can concentrate writing a song over the weekend. That means the six have to stay overnight and all the Chipmunks/Chipettes share the same bed with Lalu. Picture a babysitter sleeping with your kids...
Alvin: It's Aunt Jackie. She's making us a zesty five-course meal. Dave: Really? Well, can I talk to her? Theodore: She's practicing her pole dancing. (Alvin and Simon look at each other) Dave:Pole dancing?
Learning/practicing pole dancing has recently become a well known workout, however, so it might have been just that. It did, however, originate from strippers, so it still counts.