- Mixed with Fridge Horror. At the end of "Her Chance To Dream" you're probably left wondering why Rebeccca didn't just go with Captain Stansbury and take Molly with her. Well, Stansbury is dead. That implies that Rebecca would have to die in order to go with him, and in order for Molly to go with them, she'd have to die too.
- "For Whom The Bell Klangs". It's kinda strange the city works on musical tones. And then, why would Thaddeus E. Klang necessarily use Katie Dodd in his plans? You realize: he's a snake, and snakes have different hearing capablities than mammals.
- Baloo and his friends live in a fictional counterpart of the United States called "Usland" (never stated in-series, but according to Word of God); in their universe, the fictional version of the Soviet Union is Thembria (stated in-series). When taken together, the names can be taken as puns (us = the USA/Usland; them = the USSR/Thembria).
- In the opening movie, Baloo asks Kit to explain how he got mixed up with the pirates. Kit says that he joined up with them about a year prior to the story's events but got "sick of it". Now that begs the question: "Sick of what?" Though given that Don Carnage was willing to throw Kit off the Iron Vulture, we can probably guess.
- "Bygones" features an aged World War I combat pilot who called the Sea Duck "newfangled". Baloo responds with "The Sea Duck's 30 years old!" The show takes place in the 1930s. Something doesn't add up there...
- It slowly becomes clear that the 1930s aesthetic of the show doesn't mean it's our 1930s. Not much sign of Earthlike geography, or wildlife: one episode features the first experimental jet turbine in Cape Suzette (making it around 1944-1947 by our history), but we can't expect the show to stick closely to the history of airplane tech when higher priorities like the Rule of Cool and Rule of Funny are at stake.
- Not to mention in the episode "Your Baloo's In The Mail" where Rebecca says her mail with her contest winning ticket wasn't important because she fears Baloo won't take her request seriously, but is insistent that Baloo must use the fastest mail service around. If Rebecca had been honest with what her mail was, or if Baloo had just listened to her and realized that if someone is so insistent about using the best postal service method around then their mail must be important regardless of what else they tell you, a lot of trouble would been avoided, meaning they had two different ways to resolve the problem and in the end failed to do either which led to the Downer Ending that upset so many fans.
- A date on a newspaper and a comment on the Yankees, both found in the Plunder and Lightning pilot episode, would place the show in an alternate history 1941. Concerning the Sea Duck's age, Baloo may have been rounding up by a few years. To handwave it, you could actually just blame it all on Wildcat, the mechanic. Judging by his skill in and odd manner of fixing things, it isn't too hard to believe that there is not a single inch of the Sea Duck that was part of the original plane.
- "A Baloo Switcheroo", the episode with the soul switching idol: They cooked up a zany scheme to seed clouds, even created a hurricane by accident, in an effort to create lightning, when clearly, just a few seconds before, we are shown that the idol's power could be triggered by a mere wall socket, which is how Rebecca and Karnage are switched. Karnage's tail gets stuck in a wall socket while they both held the idol and were looking at it, yet nobody seems to notice this fact.