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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.
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...
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.