Emelius quits sending correspondence school spells to Miss Price because the book is torn in half and the rest is missing. Except he considered the whole thing to be rubbish in the first place. So he gave up a perfectly good con just because of a few missing pages?
He may not feel up to the task of making up convincing material to pad out the ending. Not everyone is good at concocting stories (or magic words) that match somebody else's style.
The animals on Naboombu seem very friendly toward Emelius and crew, the only hostile moment being at the end of the trip when Emelius has stolen the Star of Astoroth. With such friendly relations, why didn't Emelius just say, 'Hey, nice star, can we write down the words?' The king seemed to have no problem with other people touching it, provided they didn't swipe it.
Because Emelius is a con-man and a swindler. He doesn't think in terms of honesty and negotiations, he thinks in terms of sleight-of-hand and skulduggery.
Cosmic Creepers eagerly tried to attack Charlie when he was turned in to a rabbit, and yet when Emelius is transformed the cat doesn't try to make a meal out of him. Cosmic Creepers learned his lesson.
The filmmakers obviously didn't think through the fact that Miss Price's "missing page" is on the opposite side of the sheet from the one in her possession, so by all rights she should have it. It lets Angela Lansbury do a dramatic page-turn, but at what cost?
Our heroes have told the bed to take them to "The Island of Naboombu." Well, without more specific directions the magic guiding it must default to the geographical center of the island. Well, guess what? The island is crescent-shaped, so the geographical center is in Naboombu Lagoon, not any portion of the land.
Furthermore, the bed is enchanted with a traveling spell, which must have a "the traveler must survive the journey" clause. Thus the bed imbues our heroes with the (temporary) ability to breathe underwater.
In the climax, Britain is defended by the real Old Home Guard — the veterans of not just World War I, but every war in British history.
The clothes of King Charles I appear to be leading Oliver Cromwell's Roundheads into battle. They must hate the Nazis even more than they hate each other!
Seeing as the Star of Astoroth originally came from our world, why couldn't it come back into it? Because the Star's magic created the alternate world for the escaping magical animals to live in peace away from our world, & therefore won't leave while its power is still doing it! The sailor who originally found the island must have stumbled into & out of the portal the star created somewhere on the sea that transported the animal's ship to that world, but the Travelling Spell bypasses such a gateway.
Originally the moment where Professor Browne, trying to sleep at the train station, wakes to see a vision of Miss Price dressed as a magician's assistant, seems like a random Big-Lipped Alligator Moment brought on by his guilt and cowardice at leaving and his feelings for her. But just prior to this we had seen her try to call for help, only for her phone to not work and be taken from her, then be led away as a prisoner as she fails to cast the transformation spell on the Nazi colonel. So she's in danger and she very much is desperate for help; consciously she believes Browne has already left on the train but subconsciously she wishes very much that he would come to her and the kids' rescue. Even without her spells and supplies, she's still a witch, so her will could easily have been made manifest as that vision (something she knows Professor Browne would be sure to react positively to); note that among the words the vision sings is a request for a champion...
Ms. Price appears to have a knack for intuitive casting. Mr. Brown admits that he reworked the spells in the book he found, thereby negating their written power, but since Ms. Price seems to cast more by emotion backed up by incantation, for her it's not the words, but the feeling behind the casting that matters. So her doing projections seems completely within her wheel house.
Remember how the enchanted broom was out of control when Miss Price tried to fly it, and how the rabbit spell was short-lived, and moreover, failed to result in the right animal? That's probably because Emelius changed some of the magic words a little bit to fit his own style.
Why did they go to a comic book world? There's the possibility it's because that's the fairy land the animals retreated to. Another possibility is The Isle of Naboomban doesn't exist. While the magic in the book is real, the actual place may have long since fallen to ruin or been destroyed. Also, our heroes don't know anything about it save what was made from a comic book so the only place the magic can visualize is from said comic book.
Why the vulture medics are so very, very disappointed when they don't get to carry an injured player off the field.
OK, they have a lion king (no comment from the peanut gallery) temporarily changed into a rabbit, with no Star Of Astoroth on his neck to justify his authority (or even identify him, apart from the crown). Do the Naboombans revolt?! What happens to the king?! Maybe hopefully the villagers don't see him as a cute little rabbit and (at best) laugh him out of a job, if he doesn't get eaten first.
For that matter, does the magic that makes them anthrophomorphic wear out without that medal?!
Presumably the spell cast by the star was a permanent one so taking it away would not remove the animals' anthropomorphism and intellect; and if the surmise above is correct that the reason the star can't leave is because it is still maintaining the spell, then as long as the star cannot leave, the spell will remain anyway. By implication this also suggests that when the star disappeared from Browne's handkerchief, it reappeared back on Naboombu. What is not addressed, however, is—the transformation spell came from the same wizard's book and thus would presumably be stronger when it is cast in the same place his star was. Because of this, or because it's another world, might the king's change last longer—or even be permanent?
Hopefully the spell ended when the humans returned to England, same as the Animated Armor collapsed when Miss Price got knocked out.
What if Professor Browne dies in the war?! The kids are certainly left without a father figure or a dad.
The kids' previous caretaker dies after a bomb kills her from her doorstep. An explosive device laid by the Nazis at her doorstep destroys her workshop and nearly kills Eglantine. It could have been cruel irony had the Nazis succeeded.
When Miss Price first changes Charlie into a rabbit, Cosmic Creepers attacks him, and he barely escapes. Miss Price then comments that the spell was supposed to change him into a frog, which would have been even easier prey.
Remember all those cute little animals on the Isle of Nabooombu, and their cute little soccer match with all kinds of animal slapstick? Now think back to the legend that explains the origin of these islanders, in which the animals betrayed and killed what was essentially their creator, only to establish a civilization of their own. The entire visit to the island gets decidedly more ominous and creepy—shades of The Island Of Dr Moreau.