This is general Fedora issue, not a Qubes-specific issue.
Usually, this is due to network problems (especially if downloading updates over Tor) or problems with the download mirrors.
Often, the problem can be resolved by trying again on a different connection (a different Tor circuit, if using Tor) or waiting and trying again later.
Here are some examples of non-Qubes reports about this problem:
In earlier versions of Qubes, there were situations where qubes lost internet access after a TemplateVM update. The following fix should be applied in recent versions of Qubes.
For details, see the qubes-users mailing list threads [here](https://groups.google.com/d/topic/qubes-users/xPLGsAJiDW4/discussion) and [here](https://groups.google.com/d/topic/qubes-users/uN9G8hjKrGI/discussion).)
More information about this issue and solutions can be found [here](https://superuser.com/questions/951960/windows-7-sp1-windows-update-stuck-checking-for-updates).