Because as far as I know, Federation means the unity of many states type of Government just like USA, not inter countries community like United Nations.
The word federation actual has many meaning and usages, the one you cited is just one. It can also be a league like structure or a association. Basically a federation is a collection of peoples, or countries, or communities, or organizations, or groups that combine for a particular purpose.
And... a United Nations type of organization wouldn't use Federation as their name. They would simply use United Planets, not United Federation of Planets.
If you think about it, why do
they use both "united," and "federation?" Wouldn't one or the other, combined with "planets," kind of cover it?