Very simple. Before they made TLK2 and give name to cub at the end of TLK, no one, not even Disney knew anything about that cub. But since they had to give him some name at that time, they started to call him Fluffy. Since "cub at the end of TLK" is kind of long.

Then of course Fluffy went through some naming. Like authors of TLK Six New Adventures made him male and name him Kopa, which Disney ignored in making of TLK2, despite allowing them to release books. Also name Tanabi was even more popular amongst fans, again he was made male and was often featured in fan fiction at that time.

So in development of TLK2 Disney did want to use male cub at beginning, but latter after few changes, they changed Fluffy to female and she got name Kiara. Which is how they released it. So some people will say Fluffy is female, because Fluffy is actually suppose to be Kiara. Fluffy was only nickname for the cub, till Disney decided what to do with him.

But as always there are some disagreements, like some people do not believe Fluffy is Kiara. Reasons for that might vary, some point out Fluffy looks more like male, despite Disney trying to convince us it is same cub as in TLK2. Also differences between two presentations are usually pointed out. So some people believe they are not same presentation and they are not same cub. Which is why some say cub at the end of TLK is Kopa. And that Kiara happened latter. That was often base for some fan fictions which try to tell what happened to Kopa, since he is not in TLK2. There are arguments against it too, like the fact that both movies were made by different people and the fact that TLK Six New Adventures are not official, since they were not made by Disney.