[ubuntu] Update and upgrade and (?) missing files

Hi, all. I prefer to update/upgrade my *buntu machines using the proper system application (updater). But sometimes I go to the terminal and do it manually, specially to use these 3 commands:
apt-get upgrade --fix-missing
apt-get autoclean
apt-get autoremove

Why is that there are, quite frequently, missing files, libraries, whatever, in ubuntu?
I think the system updating app must be upgraded to solve this.