Update Manager should update the package database every time it is run (I doubt that it will directly call apt-get for that, more likely it uses libapt), otherwise it could not be aware of possible updates. Running
is only needed when your dependency chain is inconsistent or the package manager was not able to configure a package, most of the time that is the case after a failed installation.
May it be possible that your network connection was unreliable at that time? If not this may indeed be a bug and if it is repeatable you should report it.