These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Blame the short-lived live-action/animated companion, Little Muppet Monsters, for that one. It only lasted 3 episodes for a variety of reasons (animation not on time, clash between animation and live-action, not-so-good execution of concept (3 kid Muppets broadcasting their own TV channel, only receivable in the Muppets' own home), etc.). Yet, they kept the theme for the ending of Muppet Babies until they ended in 1991.
What's also incredibly bizarre is when you consider this series used footage from a film that later became a franchise. During the third season, there was one episode where Fozzie tells everyone of an "Attack of the Silly Tomatoes" and that sequence used footage from the 1978 film Attack of the Killer Tomatoes!. Due to its ratings success, John De Bello was called to make a sequel (10 years after the original film was made), which led to us having three more movies in the series plus the 1990-1991 Fox Kids cartoon (ironically produced by Marvel Productions).
The episode where they try to cure Beaker's fear of the dark. Everything about that episode.
The episode where they're all making cake, and it randomly cuts to the incredibly creepy Stay Puff Marshmallow Man from Ghostbusters destroying a city.
"I'll Be Blue For You." Given that it's Gonzo singing it you'd think it'd be nothing but Narm, but... damn, even as an adult it's hard not to break down into a quivering heap at this. You can imagine what it did to the kids in the audience. The fact that it's also an Ear Wormreally doesn't help matters. * Sniff!*