reassign 1042902 elpa-system-packages 1.0.11-2 thanks The variable system-packages-package-manager gets set to "pacman" because the executable path is searched for appropriate programs, and "pacman" is searched for before "apt", and so if the game pacman is installed (package pacman) and "/usr/games" is on $path because the user is just a fun loving bloke...
I'd suggest just hard-coding it to "/usr/bin/apt" in a Debian patch.