Why is it called Lilo & Stitch 2 when it's actually the third movie?
This is a direct sequel, while Stitch! The Movie takes place after this one.
Dogs in School?
Why does Kumu allow Stitch to be in his class if he isn't a student of his? Yeah, he's Lilo's "dog", but teachers don't allow pets to be brought to their classes, unless it's a veterinary class, perhaps...
Remember in the climax of the first film, Stitch was shown dancing in a competition alongside Lilo and the other girls.
Shouldn't she be banned?
How was Lilo able to participate in the competition after the mess Stitch caused during the rehearsals? Shouldn't Kumu have banned her from performing her dance after Stitch's rampage?
Kumu may have noticed that Stitch wasn't with her and that she was really committed to doing the performance without any disasters this time.
Kumu probably had a Heel Realization after the incident and allowed her to still compete.
What Happened to the Road?
When everyone is chasing Stitch's starship in the car, the road suddenly just stops and a huge chunk of it is missing. This is before the crash. Why is the road out? And with no traffic cones, dead-end signs, or crews working to fix it?
Did the Machines know?
When Stitch plans to forever in the ship, Lilo chases after him and Stitch's ship crashes on a mountain. Somehow, the machine to regenerate Stitch is already waiting for Stitch at the top of the mountain. Why is it there? How did it get there?
It was on the ship. Jumba was using the ship as his laboratory (since it wasn't being used for anything else). When the group sees the ship taking off, Nani exclaims "the ship!" while Jumba exclaims "the fusion chamber" which all but outright says that the fusion chamber is in the ship. The real question is how it happened to be the one thing besides Stitch himself that survived the crash intact...
Possible idiot moment?
In Lilo & Stitch 2: Stitch Has a Glitch, it seems that a lot of the problems are caused by everybody not knowing what is wrong with Stitch. Except Pleakley and Jumba know about the whole "molecules aren't charged" thing. So why didn't either of them tell Lilo or Nani about Stitch's issue? Seems like a plot hole to me.
Because they didn't want to worry them with how serious the situation was, especially since they intended to fix it quick as possible. Besides, when one of the people is a Mad Scientist who probably spent a lot of time prior to the movies on his own and the other is... Pleakley, rational plans built on common sense sometimes don't come up.
Also in Lilo & Stitch 2: Stitch Has a Glitch, around the end, Stitch's plane crashes on a random mountain and Lilo rides her hover car there. For no reason at all, the recovery pad to heal Stitch is already there when she arrives. Why?
On Earth, Jumba's spaceship is his lab, so the fusion chamber was already on-board as it was built in there. When the ship crashed, the fusion chamber most likely got knocked loose and fell out, perching on the mountain. Of course, it is strange that the thing was upright and completely unscathed when it landed there.
Jumba using Stitch's name.
Why does Jumba call Stitch by his name here? In all other media, he refers to him as "626" and It's not that he dislikes the name, he always seems to call people by descriptions. (Lilo is "Little girl" Nani is "Bigger girl" Etc)
Lilo & Stitch 2 and Lilo & Stitch: The Series were handled by different animation studios (Disneytoon Studios for the former and Disney Television Animation for the latter) and they didn't really speak to one another for consistency. In fact, Jess Winfield (an executive producer of The Series) said they only had one meeting together in their pre-productions to make sure they weren't copying each other's story ideas for their films (Stitch! The Movie was also under development back then), but Disneytoon possibly also interpreted this as "don't copy what The Series is doing". He also claimed that during the development of Leroy & Stitch, his team got to look at an early cut of Lilo & Stitch 2, and he and his team pointed out several continuity errors, which Disneytoon most likely didn't correct. That all being said, Jumba does refer to Stitch by the name Lilo gave him at times even in The Series, so...
What happened to the roof?
In the scene where Lilo and Nani are stargazing, why is the roof of Lilo and Stitch's dome suddenly missing? On my first viewing, I initially thought it was the moon roof we see in the TV Series (where they can push a button and a skylight opens up on the top of the dome), but no, half of the dome is gone. Is the whole roof retractable? Was this supposed to be symbolic of something?
where Lilo and Nani are stargazing, why is the roof of Lilo and Stitch's dome suddenly missing? On my first viewing, I initially thought it was the moon roof we see in the TV Series (where they can push a button and a skylight opens up on the top of the dome), but no, half of the dome is gone. Is the whole roof retractable? Was this supposed to be symbolic of something?