Eu tive o mesmo problema. Para mim, a solução foi:
rm /etc/apt/apt.conf.d/50appstream
A fonte: O Ubuntu 16.04 apt-get update não funciona com repositório local
Usando o apt-mirror, eu fiz o download dos pacotes xenial para minha máquina (endereço IP: 172.16.3.37). O conteúdo da minha "mirror.list" para o apt-mirror é o seguinte.
############# config ##################
#
set base_path /ubuntuRepo
#
# 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 ##############
deb-amd64 http://archive.ubuntu.com/ubuntu xenial main restricted universe multiverse free non-free
deb-amd64 http://archive.ubuntu.com/ubuntu xenial-security main restricted universe multiverse free non-free
deb-amd64 http://archive.ubuntu.com/ubuntu xenial-updates main restricted universe multiverse free non-free
deb-amd64 http://archive.ubuntu.com/ubuntu xenial-proposed main restricted universe multiverse free non-free
deb-amd64 http://archive.ubuntu.com/ubuntu xenial-backports main restricted universe multiverse free non-free
deb-i386 http://archive.ubuntu.com/ubuntu xenial main restricted universe multiverse free non-free
deb-i386 http://archive.ubuntu.com/ubuntu xenial-security main restricted universe multiverse free non-free
deb-i386 http://archive.ubuntu.com/ubuntu xenial-updates main restricted universe multiverse free non-free
deb-i386 http://archive.ubuntu.com/ubuntu xenial-proposed main restricted universe multiverse free non-free
deb-i386 http://archive.ubuntu.com/ubuntu xenial-backports main restricted universe multiverse free non-free
Os arquivos foram baixados com sucesso.
Eu tentei instalar pacotes usando este repositório de outra máquina. O arquivo /etc/apt/sources.list da máquina contém a seguinte linha (intencionalmente mantive apenas uma linha para reduzir o número de erros).
deb http://archive.ubuntu.com/ubuntu xenial main restricted universe multiverse free non-free
Agora, quando eu tento "apt-get update" estou recebendo o seguinte.
Get:1 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial InRelease [247 kB]
Ign:2 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main amd64 Packages
Ign:3 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main i386 Packages
Ign:4 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main Translation-en
Ign:5 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:6 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main DEP-11 64x64 Icons
Ign:7 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
Ign:8 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe i386 Packages
Ign:9 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe Translation-en
Ign:10 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe amd64 DEP-11 Metadata
Ign:11 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe DEP-11 64x64 Icons
Get:2 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main amd64 Packages [1,201 kB]
Get:3 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main i386 Packages [1,196 kB]
Get:4 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main Translation-en [568 kB]
Ign:5 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main amd64 DEP-11 Metadata
Ign:6 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main DEP-11 64x64 Icons
Get:7 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe amd64 Packages [7,532 kB]
Get:8 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe i386 Packages [7,512 kB]
Get:9 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe Translation-en [4,354 kB]
Ign:10 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe amd64 DEP-11 Metadata
Ign:11 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe DEP-11 64x64 Icons
Err:5 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main amd64 DEP-11 Metadata
404 Not Found
Err:6 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/main DEP-11 64x64 Icons
404 Not Found
Err:10 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe amd64 DEP-11 Metadata
404 Not Found
Err:11 http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu xenial/universe DEP-11 64x64 Icons
404 Not Found
Fetched 247 kB in 0s (574 kB/s)
Reading package lists... Done
E: Failed to fetch http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu/dists/xenial/main/dep11/Components-amd64.yml 404 Not Found
E: Failed to fetch http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu/dists/xenial/main/dep11/icons-64x64.tar 404 Not Found
E: Failed to fetch http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu/dists/xenial/universe/dep11/Components-amd64.yml 404 Not Found
E: Failed to fetch http://172.16.3.37/ubuntuRepo/mirror/archive.ubuntu.com/ubuntu/dists/xenial/universe/dep11/icons-64x64.tar 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.
Eu fiz uma pergunta semelhante aqui . Qualquer pensamento útil é muito apreciado.
Eu tive o mesmo problema. Para mim, a solução foi:
rm /etc/apt/apt.conf.d/50appstream
A fonte: O Ubuntu 16.04 apt-get update não funciona com repositório local
Parece que o seu repositório espelha apenas os pacotes amd64, mas o seu sistema quer os pacotes amd64 e i386. Basta adicionar deb-i386 linhas semelhantes às deb-amd64 que você já tem e sincronizar o espelho novamente.