Fridge Brilliance: The "big bones" comments are referring to surface-dweller Kathy's thick, healthy, high-calcium bones. There's not much vitamin D and calcium in a sunlight- and dairy-free underground society. (Which raises the question of how Gus got to be so tall.)
Hollywood Homely: Wanda is supposed to be nerdy, frumpy and awkward, with dorky glasses and bad hair. She's also played by Kathy freakin' Ireland. Mike and 'bots got a lot of mileage in this film out of her day job.
Uncanny Valley: Kathy Ireland's voice, again. She sounds more like a five-year-old girl than a 5'10" woman, making already narmy lines like "Bitchin'" sound disturbing.
The sequel Journey to the Center of the Earth provides examples of:
Big-Lipped Alligator Moment: At one point, the main characters have several odd dream sequences. They appear to be scenes from either the movie that didn't get made (see above quote from the original director), or else scenes from abandoned character arcs (as it seems clear from viewing the movie, several actors also bailed on the movie).