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 pelikula don't have such, as all you have to do is pay attention to what is sinabi and how it is said, and at some points to use common sense.
1.) The cub's disensyo 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 pelikula - basically we just have to accept that...