Немного изменил файл mirror.list
############# config ##################
#
set base_path /var/apt-mirror
#
set mirror_path $base_path/mirror
set skel_path $base_path/skel
set var_path $base_path/var
# set cleanscript $var_path/clean.sh
# set defaultarch <running host architecture>
# set postmirror_script $var_path/postmirror.sh
# set run_postmirror 0
set nthreads 20
set _tilde 0
#
############# end config ##############
###### Ubuntu Main
deb http://archive.ubuntu.com/ubuntu/ bionic main restricted universe multiverse
deb-src http://archive.ubuntu.com/ubuntu/ bionic main restricted universe multiverse
###### Ubuntu Update
deb http://archive.ubuntu.com/ubuntu/ bionic-security main restricted universe multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-updates main restricted universe multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-proposed main restricted universe multiverse
deb http://archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
deb-src http://archive.ubuntu.com/ubuntu/ bionic-security main restricted universe multiverse
deb-src http://archive.ubuntu.com/ubuntu/ bionic-updates main restricted universe multiverse
deb-src http://archive.ubuntu.com/ubuntu/ bionic-proposed main restricted universe multiverse
deb-src http://archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
После перезапуска apt-mirror начал работать нормально, пакеты скачиваются. Если честно не углублялся в причины, но в таком виде конфиг работает.
