I really wonder how do people see "so many plot holes"? Because I can see ONLY TWO and even they are relative.
A plot hole is something that causes the plot or a part of the plot to not add up or to not make sense. These two movies don't have such, as all you have to do is pay attention to what is said and how it is said, and at some points to use common sense.
1.) The cub's design and the ceremony.
But officially that is not a plot hole. As Disney has made it official it is "Fluffy"/Kiara in the movie universe. As in introduced no one else in the movies - basically we just have to accept that...
In the original script (which was started 2-3 years before Simba's Pride was released) there were no Outlanders. It was only Zira (then known as Bianca), Kovu, and the three hyenas. In this script, Kovu was Scar's son. This was changed because if Zira was Scar's mate, then why would she team up with the hyenas, who killed Scar. They also had to change the fact of Kovu being Scar's son because that would be bordering on incest. (It would make Kovu and Kiara second cousins.)
Kathleen Turner was originally going to be the voice of Zira. Christian Slater was going to do the voice of Adult Kovu.