Worse, if an app is updated whilst it's running, it can cause arbitrary crashes and data corruption.
I'm really glad Linux is finally moving beyond the curse of apt-get. I wrote a framework a long time ago for building distro-neutral binary installer/package hybrids and eventually walked away ... back then Ubuntu was brand new and Shuttleworth was even warm to the idea, but the old guard he had to deal with hated the idea. Other distributors were even worse. They had all bought into the idea that the way Linux managed software was awesome and superior to every other OS, even as new operating systems were designed and shipped that universally did not use it.