In the second movie, shouldn't Marnie, Aggie and Luke have more time to work out their subplot, since time goes slower in Halloweentown? But at least in the present scenes the whole world is under the Gray Spell, which could be "normalizing" all magic, including the time difference.
In the third movie Grandma Aggie claims to have met Shakespeare, da Vinci et al., but these are all famous people in the mortal world. How exactly did she have time to collect all these funny anecdotes about famous people if she was in this dimension for one day a year at most?
Second movie, basic San Dimas Time issue: they only have until midnight to get back to the mortal world! Except, you know, they have time travel. Just go back in time a few minutes (like you did before, by accident) and fix everything. Or for that matter, when you're in the Timeline, just get off a little early, and you could have hours to stop Kal before you even knew he was a threat.
Fridge Brilliance on that: Time flows differently in Halloweentown than in the mortal world. There really are two clocks in play here, so to speak: The Halloweentown clock and the mortal clock. What this creates is a rare justified case of San Dimas Time: They're travelling through time on the Halloweentown clock, allowing them to access any point in Halloweentown history. (Notice that even though the timeline depicts the count in mortal years, they're still in Halloweentown when they exit.) Meanwhile, the mortal world clock is moving forward the same way it always does. The portal closes at midnight mortal world time, not Halloweentown time. They could jump off the timeline three centuries before Kal ever enacted his plan and they'd still have only a handful of minutes in mortal time to go through the portal and stop him. Basically, San Dimas Time occurs because the timeline only allows for manipulation of the Halloweentown clock.
And now for a piece of Fridge Logic mentioned immediately above: Why does Halloweentown seem to count time according to mortal years? (Notice when Luke and Marnie travel through the timeline, it shows years like 1340, 1350, and 1360 going by.) But given that Halloweentown was created after creatures and humans had a falling out, it's probably only been around for about six hundred years, give or take. Shouldn't Halloweentown years be counted from the actual creation of that world?
Actually, never mind that. I rewatched the film and Gort explicitly says that the timeline is counting mortal years.
In the first movie you need the bus to go between the mortal world and Halloweentown; it's a plot point, because Gwen wants to go home immediately but the bus isn't working. But in the second movie on, any witch or warlock can summon a portal with a spell. Why didn't Gwen try that?
How exactly did Gwen and her late husband's romance work? They met at a Halloween party...and then had their second date a year later? Or did Gwen get stuck in the mortal world by accident and just decide that she liked it? Did they meet year after year, just elope on a whim, what?
Grandma Aggie clearly has a bag of holding in the first two movies. Yet in the third, a primary source of tension is that her magically-alive reptile-skin bag keeps trying to explore and eat things. What happened to the first bag? And why would she replace it?
As a witch with all her powers, Gwen has a lifespan of 1000+ years, yet in the first film she's bound and determined that all of her children are going to be regular humans. This means that she would stay relatively young while her children grew old and died, and she knows it. Maybe Marnie wasn't off the mark with her jab about Gwen getting tired of her kids and disowning them eventually after all.
But on the other hand, she's presumably aged fairly significantly her +10 years in the mortal world...right? Wouldn't people eventually notice if she didn't?
Not entirely sure if this is what the previous person was getting at, but maybe being in the mortal world (or possibly, not doing magic) makes her age like a mortal would. Also, maybe the reason she doesn't use magic very often is because she doesn't want to live for centuries more without her husband?
How old was Gwen when she met her husband? She crashed a Halloween party, but she could have been anywhere from late teens/early twenties to centuries old. Mayfly-December Romance, anyone? And if she actually does have a 1000+ years lifespan, then she knew going into it that her husband would die long before her, too.
For a supposedly good witch, Aggie has a couple of less than savory spells in that book of hers. (The Grey Spell and the Creature Spell, for example.) Kinda makes you wonder if there was a time when her use of her powers wasn't so benevolent.