A major plothole, though not technically a fatal one, as I'll explain soon, is that it seems that none of the wildebeasts implicated the hyenas in causing the stampede. If they had, then it would be a HUGE red flag if they had caused the stampede that killed Mufasa (and supposedly Simba) only for Scar to immediately overturn Mufasa's ban on them being in the Pridelands and let them all in.
Of course, it's quite probable that Scar had in mind that IF anyone mentioned that the hyenas caused the stampede that killed Mufasa, that he would say that they did it to get back at Mufasa for their run in with him in the Elephant Graveyard and would order the Pridelands lionesses to kill all the hyenas.
Now, if they tried to rat out Scar, he could simply say that they were lying. As poorly as he disguised his dislike for Mufasa, nothing had really been there to tie to him to either the attack in the Elephant Graveyard or the stampede, at least, that wasn't kept solely between himself, the hyenas, and, well, Mufasa, who found out too late to tell anyone. It's not that unusual for dictators to take out their own minions once seizing power.
I think that, since nobody did tie the hyenas to the stampede, that Scar felt his best option was to keep his promise to the hyenas and let them in and keep them as his own personal army.