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It's normal, I get the same thing. The important thing is that when you try to install a package it installs the right one (x86_64). I give you an example using YUM: yum search vlc-core I get this: vlc-core.i686 vlc-core.x86_4 but when I do yum install vlc-core It automatically installs the x86_64 version.

Anyway, if you use the default Fedora package manager (the graphical one) it only shows the packages for your machine's architecture.