@milan Also gnome software now has an annoying config that when you have a package available from the system repos and flatpak it will show you the flatpak version first. In the upper right corner were it says flatpak, it is a drop down button that you can use to select either Flatpak or system package.
But Flatpak is the default. I am not a fan of this change, and it leads people in one direction; a third party package system over the system default package manager.
@joao Yea sometimes (mainly before the updates after installing Fedora) it behaves like this, but now it is all over the place. Some packages have duplicated entries, sometimes it's just the flatpak and nothing else is in the dropdown and the duplicate entry is missing. the other entry may also state the wrong package version.