I don't think so. This is my attempt to disprove the claimed plot holes.
Now, I'm not saying this film doesn't have some problems. Because it does. I'm only saying that I don't think it has plot holes. Most of the following arguments I originally posted at IMDB message board in a debate, as VampireOutlaw.
You see, if something that's left untold does not affect the plot at all, then it's not a hole in the story but only something that could be further explained just for the interest of it.
I'm starting to think this film does not have plot holes at all - that its only continuity problem is that they remade the ceremony scene and the cub's design.
I think I can disprove the claimed plot holes:
"Kiara looks entirely different from the cub at the end of TLK, and the ceremonies are also obviously different. What happened to the other cub?"
There is no other cub; on the first film's commentary track, that ending cub was refered to as "Fluffy" with no decided gender, and then in this film's official trailer they used "Fluffy" as baby Kiara, and in a magazine interview confirmed that "Fluffy" and Kiara are the same character. So in fact this is not a plot hole but a visual continuity problem.
Is it a plot hole because the film itself doesn't literally say that "Fluffy" and Kiara are one? I don't think so, because this film doesn't make any reference to any other cub but Kiara, therefore she and "Fluffy" unavoidably blend into one. On the contrary, if they were supposed to be two different cubs, this entire movie would be one huge plot hole.
But as Simba and Nala had only one child in the movie universe storyline, the stupid visual difference remains only a visual paradox, not a plot hole.
"How does Nala know Vitani?"
Remember that Vitani was born during Scar's reign which the first movie skipped over. And as Kovu was the last born and hand-chosen by Scar, it's likely Vitani and Kovu were older than new-borns before the end.
Therefore it is entirely possible, perhaps even likely seeing to that Nala knows Vitani, that Nala met Vitani before she left to find help and ran into Simba. She may have met Vitani also as Vitani left to exile with her family - after all Nala was the queen.
So, after all this isn't a plot hole any more than the exile is. The indicated event just happened during a time period even the first film skipped over while the sequel chose to start off where the first film left us.
The important thing is that the sequel confirms that both Nala and Vitani were in the Pridelands during that skipped-over time period. That confirmation keeps the later indication of them having met from being an actual plot hole, and makes it nothing more but a not-specifically explained situation.
"Where was Zira in the original?"
The sequel implies that she and the otehrs were supposed to be in the Pridelands at that time, and their total lack of screen time in the first film IS supported by its content. Remember how Simba told Nala to rally up the lionesses? Well, obviously Nala didn't rally up all of them and the sequel makes it clear why, by having those that weren't raalied up, obviously siding with Scar. It's not like the good guys didn't have enough challenge in dealing with the huge hyena pack that still sided with Scar.
This results in the films' contents combined explaining that they were in Pridelands but weren't called upon at Simba's return because they would've made the enemy that much more powerful. Where in Pridelands they were exactly, isn't important. Therefore, not a plot hole but only a not-throroughly explained situation.
"Where did the Outsiders come from? There was no mention in the first movie at all about ANY lionesses who favored Scars' opinion...and I think this is the biggest plot hole of them all. No lionesses that followed Scar. So where did they come from?"
Remember the films are supposed to form one entity. So the first mention coming in the sequel's half of that one entity, does work, because the first half doesn't deny this matter nor make it impossible. Hence, them not appearing in the first half of the entity is explained by the content, and them still supporting Scar is explained by the fact that so did the hyenas.
The fact that they didn't show how Simba met the to-be-Outlanders, isn't a plot hole eiteher because it happened during the time even the first film skipped over and the sequel chose to start off where the first film left us.
How did the Outlanders first come to the Pridelands? They aren't seen in the first film at any point.
This detail does not affect the sequel's plot nor their role in it in any way. All that matters to it is that they sided with Scar or were believed to through prejudice. Their origin prior to Pridelands era is only a matter of interest, therefore not a plot hole.
"Who was Kovu's father?"
Not a plot hole because Kovu's father's identity is completely irrelevant. We are told that it isn't Scar but that Scar adopted him as his heir, that's all the plot needs in order for the viewer to understand his character as well as Nuka and Simba and the story.
"If Kovu's father's identity is irrelevant, then how did Zira end up with him? I mean, she had two able cubs of her own."
Or one. Vitani may well be Kovu's litter mate. Actually, it's entirely possible all Zira's cubs were from the same father. After all we don't know anything about their timeline in Pridelands except that Kovu was the last born.
Anyway, how did Zira end up with Kovu's father is naturally irrelevant too, by his father's identity being irrelevant. It just doesn't matter to the story SP wants to tell. All the story needs to work perfectly logically is the information of how does Kovu relate to the first film's events, is he Scar's kid or not, and what is his purpose in the sequel. And that information is given in the film.
Do not bother coming to argue the topic of Kovu's parentage with the Darrell Rooney Facebook post. That post is not factual information so long as it isn't confirmed on an official site. Just because FB staff bans people who impersonate famous people, if revealed, doesn't mean people aren't doing it. A ban is hardly a threat enough to stop such practice, as one can easily create a new account from another computer. And even if that post proved to be genuine, the man said "was" and "if I remember correctly", making the matter only that Kovu may have been at one point intented as an orphan. But as for now, there's nothing official on that whatsoever. Therefore, officially, Kovu has never been described as an orphan and Zira is Kovu's biological mother.
So, Kovu's parentage stuff doesn't create any plot holes and there are no official answers to the open matters.
"How could he have been hand chosen by Scar?"
"Kovu was the last born before you exiled us to the Outlands" "He was hand-chosen by Scar to follow in his paw prints and become king" = clearly setting Kovu's birth to a time before Simba returned and Scar was still alive. Naturally Kovu'd have to be older than Kiara, but hey, the film never said he isn't. The fact that he appears the same age as Kiara, doesn't mean that he was.
So I see absolutely no quesion as for how Scar could've hand-chosen him.
"Why was he hand chosen by Scar?"
Why do people choose anything? Because they feel the person/thing is worthy of the thing they're chosen for. Any more detailed reason is not significant to the story. I really don't know why this should be a question. Especially as the first film doesn't make any reference to Scar having or even planning to have biological children. So, keeping in mind that first point I made, him choosing someone else's kid as his heir really doesn't need to be a question.
"Where is Sarabi?"
Sarabi would become a plot hole only if they'd said that she is not somerhere in there but not tell why. So this is not a plot hole, as just because she isn't mentioned, doesn't mean that she wasn't around. Obviously there was no need for her in the story SP wanted to tell, they may have left her into the background and not bother pointing her out.
"Why did Simba choose a daughter to rule the pridelands when traditionally it's always been male?"
Nothing in the first film ever said that a male is a tradition for s ruler. All the film says is that the great kings of the past are watching from the stars. All the film shows about traditions, is that it's the first born. And even if it had labeled male as a tradition, it has an entire song sequence about Simba planning to do everything his way once he'd be the king. And just before that song he said about anoteher tradition: "When I'm king, that'll be the first thing to go."
Hence, hence, not a plot hole.
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Anything else? Feel free to throw potential plot holes at me. I'd like to try and disprove them. :D Because it's fun as it is, and I think this sequel is underrated. ;)