I can't say I've every had that happen to me or anyone else I've dealt with. Do you have any references to relevant bugs/issues? A properly running package manager should not allow this unless there is a serious bug in the packages themselves.

The closest I can think of otherwise is someone getting locked out of a remote machine where root was the only active account and was authenticated buy user/pass not by key, and he accepted the "start blocking password logins for root" change in a distribution upgrade (so he was warned so his own fault!).

I've never had that happen, but thankfully remote (virtual) serial consoles are commonplace. Something I wish was more common in Windows environments, as I've had remote access dump on Windows many times, leaving me with no options other than a long drive or call in to a remote DC.