Regarding Characterization Marches On: It makes sense that Apple Bloom would appear to be the "only sane mare" in this incident. She's probably too young to have bought into the rumors connected to Zecora, and not yet been given a reason to obsess over her cutie marks.
Twilight disregarding the rumors at first makes sense when you remember that because she didn't have friends until she came to Ponyville, she doesn't know anything about gossiping - she only believed what she'd seen for herself or read in books.
The Cross Cultural Kerfuffle of the ponies mistaking Zecora's pawing at the ground for water as a threat display makes a lot of sense when you remember that, at the very least, Twilight and Nightmare Moon pawed at the ground before charging each other in the second episode. In other words, pawing at the ground is a threat display amongst ponykind, even if to zebras it's more of a nervous tic.
Evidently, Spike had no idea "Rainbow Crash" was an insulting nickname for Rainbow Dash during her fillyhood days until "Sonic Rainboom" came along. It makes perfect sense that since Spike wasn't around then, he wouldn't have known it from the start.