Idiot Plot: The Termite episode requires you to accept that that K'nuckles forgot that he can take off his legs in order to make any sense. Or he is too stubborn. Scratch that, more than half of the episodes require that you accept K'nuckle's lack of understanding of anything to mindblowing extremes.
Memetic Molester: Dr. Barber is commonly depicted in fanart and fanfics as a pedophile, often in regards to Flapjack. To a lesser extent, Captain K'nuckles and Lolly Poopdeck are subject to this trope as well.
Captain K'Nuckles. In one episode, his love interest left him because she found him unattractive, when in actual fact - aside from the frequent Gross-Up Close-Up - he's got a very simple, very appealing design.
What Do You Mean, It's for Kids?: The series is ostensibly meant for a young audience, and at first glance it really doesn't look like it's not. After a few episodes though, the large quantities of Surreal Horror, graphic Body Horror and dark humor were and still are more than a bit unnerving for its target demographic.
The Woobie: Flapjack has his moments, usually whenever he's sad.