This is probably Robert Rodriguez's Shorts
In a gambit that seems designed to amuse the filmmaker more than his audience, the story is divided into five "shorts," which are presented out of order. The central character is grade-schooler Toby "Toe" Thompson (Jimmy Bennett), who lives with his overworked parents (Leslie Mann and Jon Cryer) and disdainful teenage sister (Kat Dennings).
Toe appears in all the stories, but several of them feature other families in the Thompsons's Texas subdivision, Black Falls. It's a newfangled company town whose residents all work for the same man: greedy, tyrannical Carbon Black (James Spader), who markets a shape-shifting PDA that can do, well, almost anything. (Battery life is lousy, though.)
For no reason the movie bothers to imagine, the suburb is suddenly blessed with a magical alternative to the PDA: a rainbow-striped rock that grants wishes. Shock, chaos and mild hilarity ensue as the object passes through many hands. Some people make their wishes carelessly; others idly wish without knowing that the rock will fulfill their request.
Friendless Toe wears braces and is tormented every school day by a gang led by Carbon Black's daughter, Helvetica. (She's played by Jolie Vanier, who might have been cloned from the Addams Family-era Christina Ricci.) Toe and "Hel" contend for the rainbow rock, which is ultimately seized by the girl's father. He, of course, needs to learn a few lessons in humility and humanity.
As the tale hops forward and backward, the magic stone falls temporarily under the control of adventurous Loogie (Trevor Gagnon), who summons crocodiles, cobras and a pterodactyl. (His surname, by the way, is Short.) The rock also creates a Ghostbusters-style monster out of nasal mucus excavated by Nose (Jake Short), the son of a germophobic scientist (William H. Macy).
Found with a search for film wishes instruction book germophobe scientist