emacs loads a special conf-mode, when, for example, opening /etc/lilo.conf. That's good. It highlights the syntax and would allow some commands like "comment-region".
Suggestion: emacs should also use conf-unix-mode or conf-space-mode (or some other suitable one) for APT configuration files, in particular, for /etc/apt/sources.list and /etc/apt/sources.list.d/*: "comment-region" is a very needed command there (as well highlighting which helps distinguish commented and uncommented strings).
I think, this is no emacs bug. Use
# -*- Mode: conf -*-
in top of this files.
Perhaps this is bug of `rpm -qf /etc/apt/sources.list.d/*`
Закрываю баг, как не являющийся ошибкой emacs.