Just wanted to post in case others stumble onto this little annoyance.
If you get a "command not found" error from bash while updating your system, bash will "hang" while pk-command-not-found is trying to query for a similar command (pk-command-not-found is a handler command ran by bash on FC12 when you try to run a command that does not exist). You can either simply accept this behaviour and wait until yum-based stuff have all exited, or you can instruct PackageKit to not perform this check at all. Even when everything is Working Properly(TM), it still might take a bit of time for the bash to return to prompt after such a query. As such, disabling this may be something you want to do anyways. Change the SoftwareSourceSearch parameter in /etc/PackageKit/CommandNotFound.conf to false:
# sed -i 's/SoftwareSourceSearch=true/SoftwareSourceSearch=false/' /etc/PackageKit/CommandNotFound.conf
Hope this helps!