The baby crocodile hatched is the same one in Peter Pan that torments Captain Hook, as seen as the baby crocodile eats a clock and chases James.
It is the first Tinker Bell film to feature pre-existing characters from the Peter Pan franchise besides Tinker Bell herself (Smee, Captain Hook, and Tick-Tock the Crocodile).
When James brings the captain her tea, it's Earl Grey "hot." This is how Captain Picard takes him on Star Trek: The Next Generation.
A short clip at 1:09:29 shows James the cabin boy surfacing with a hook, foreshadowing his future as Captain Hook.
Zarina is a dust-keeper, the same occupation as Terence, who has a crush on Tinker Bell.