Major Plot hole: Mufasa could not have been killed in the stampede....and we will show you through the magical powers of mathematics !
When the hyenas scare the Wildebeest herd, we can see that it is a very big herd with at least hundreds of heads if not more - and thus a very potent danger to kill Simba.
However, it is quickly shown that all of the herd is already in the gorge even before Mufasa arrives to save his son. But the tricky thing is that the stampede sequence lasts for an additional 3 minutes even after the last wildebeest is shown entering the gorge.
By carefully looking at the herd, we can conservatively observe that it moves in lines of about 25 wildebeests, all of which passing by Simba every 0.5 second. With that calculation in mind, we can conclude that, at the very least, the stampede requires THREE THOUSAND wildebeests for every minute it continues and we are treated with at least 3 minutes of real-time action where the stampede is functional. What it means is that in order for Mufasa to die in the Stampede, it would require at least NINE THOUSAND wildebeests - which is shown to be completely impossible.
Based on the evidence presented in the film, Mufasa was not even needed to save his son - the little tree he desperately clung-on to was enough, because a few hundred wildebeest would make a 30 second stampede in the wide gorge.
Major Plot hole: Dead Mufasa shows up in the sky to talk to his son. Great advice Pop ! Where you busy in heaven for the last few years ? Is that why you showed up only now when I am a grown adult and my kingdom has collapsed to shit ? Hopefully this will be counter-balanced with a valuable information: like a secret animal army, a safe passageway to....Oh no ? You show up for 15 seconds to tell me to remember who I am ? Great. Is this your way to punish me by pile-driving my face into a liquid guilt puddle ? Thanks Dad !
Major Plot hole: There is no logical reason for Timon and Pumba to follow Simba into the Pridelands. There are consistently shown in the first part of the movie to only care about themselves. Hell, their own philosophy, Hakuna Matata, was pretty clear. There was simply no character arc nor revelation that would make these two characters leave their peaceful lives to help others. They were simply brought along - because the movie needed their comic reliefs.
Major Plot hole: When Simba shows up in Prideland to confront Scar, none of the lionesses react to the fact that Scar told them years ago that Simba died in the stampede too. There are very concerned about Scar's allegation that Mufasa died because of Simba but no one mentions the simple obvious-to-the-face problem that all those years they assumed Simba was dead because Scar lied to them. Wake-up from the Matrix lionesses !!
Major Plot hole: Why doesn't Scar kill Simba immediately after the stampede? Why does he entrust this extremely important task to the hyenas he clearly has little faith in? It's not CSI - they are lions. No DNA tests, no security camera footage, no forensic experts, you name it. He could have smashed Simba's head againt his dad's own corpse and no one would have ever known - except for the now-traumatized hyenas.
Plot contrivence: In the Stampede scene, Zazu screams that he will find help and quickly gets bitch-slapped by Pimp Scar against a wall. Later on, he never seems to question the fact that he got hit by something, even if there was no one around but Scar and that the animal in question had a lot to gain from Mufasa's death. (This complete lack of brain lasts for years and informs us he probably developed brain cancer- may God rest his soul in peace).
Plot contrivence: When Scar reveals that he was Simba's father murderer, Simba gets some XP that he can spend on the ''jumping without my legs touching anything'' skill - which he promptly uses to kick his evil uncle's ass even though he was hanging for dear life a few seconds earlier.