Could the issue be that every single file can be pulled from a different mirror? E.g. when packages list is pulled form one mirror, the content hashes from another one and the final package again from another one, it is easily possible that one does not match as for sure not all mirrors sync and have caches emptied exactly the same time. E.g. here my apt update which pulls from various different mirrors:
Get:5 https://minio.k-space.ee/armbian/apt buster InRelease [18.3 kB]
Get:6 https://minio.k-space.ee/armbian/apt buster/main armhf Packages [591 kB]
Ign:6 https://minio.k-space.ee/armbian/apt buster/main armhf Packages
Get:7 https://minio.k-space.ee/armbian/apt buster/main arm64 Packages [698 kB]
Ign:7 https://minio.k-space.ee/armbian/apt buster/main arm64 Packages
Ign:7 https://apt.armbian.com buster/main arm64 Packages
Ign:7 https://apt.armbian.com buster/main arm64 Packages
Get:8 https://minio.k-space.ee/armbian/apt buster/main arm64 Contents (deb) [11.2 MB]
Ign:8 https://minio.k-space.ee/armbian/apt buster/main arm64 Contents (deb)
Get:9 https://minio.k-space.ee/armbian/apt buster/main armhf Contents (deb) [17.3 MB]
Ign:9 https://minio.k-space.ee/armbian/apt buster/main armhf Contents (deb)
Get:6 https://us.mirrors.fossho.st/armbian/apt buster/main armhf Packages [591 kB]
Err:6 https://us.mirrors.fossho.st/armbian/apt buster/main armhf Packages
File has unexpected size (591174 != 590754). Mirror sync in progress? [IP: 23.237.182.68 443]
Hashes of expected file:
- Filesize:590754 [weak]
- SHA512:bb903949666449552cda361ee24d4d0579baa72915b5fb3d7418acede319562ce4b93a15bf7605ae270bd9f0e59ececf622fea1365e8aa7a3d8339e2a2644f56
- SHA256:d822f1c4a63ce566baa27d1f5c523057c1d295222f097b072dc8fbeb14a29bc3
- SHA1:0f37871329a6a28cf7c53dd6ffd952342432c7ed [weak]
- MD5Sum:517fa48fb23e17f6c94248da6ce5b44b [weak]
Release file created at: Sat, 12 Dec 2020 15:07:27 +0000
Get:7 https://armbian.systemonachip.net/apt buster/main arm64 Packages [3941 kB]
Err:7 https://armbian.systemonachip.net/apt buster/main arm64 Packages
Get:8 https://mirrors.dotsrc.org/armbian-apt buster/main arm64 Contents (deb) [11.2 MB]
Err:8 https://mirrors.dotsrc.org/armbian-apt buster/main arm64 Contents (deb)
Get:9 https://armbian.tnahosting.net/apt buster/main armhf Contents (deb) [17.3 MB]
Err:9 https://armbian.tnahosting.net/apt buster/main armhf Contents (deb)
Fetched 18.3 kB in 55s (332 B/s)
Reading package lists... Done
E: Failed to fetch https://us.mirrors.fossho.st/armbian/apt/dists/buster/main/binary-armhf/Packages.bz2 File has unexpected size (591174 != 590754). Mirror sync in progress? [IP: 23.237.182.68 443]
Hashes of expected file:
- Filesize:590754 [weak]
- SHA512:bb903949666449552cda361ee24d4d0579baa72915b5fb3d7418acede319562ce4b93a15bf7605ae270bd9f0e59ececf622fea1365e8aa7a3d8339e2a2644f56
- SHA256:d822f1c4a63ce566baa27d1f5c523057c1d295222f097b072dc8fbeb14a29bc3
- SHA1:0f37871329a6a28cf7c53dd6ffd952342432c7ed [weak]
- MD5Sum:517fa48fb23e17f6c94248da6ce5b44b [weak]
Release file created at: Sat, 12 Dec 2020 15:07:27 +0000
E: Failed to fetch https://armbian.systemonachip.net/apt/dists/buster/main/binary-arm64/Packages
E: Failed to fetch https://mirrors.dotsrc.org/armbian-apt/dists/buster/main/Contents-arm64.gz
E: Failed to fetch https://armbian.tnahosting.net/apt/dists/buster/main/Contents-armhf.gz
E: Some index files failed to download. They have been ignored, or old ones used instead.
The reported successful update from @dispo above was one case where everything was pulled from the same mirrors.netix.net mirror.
I'm not sure how e.g. Debian handles this, but it makes IMO sense that somehow tie a client to a fixed mirror for a certain time.
Although I just compared the files of three mirrors and they all match, synced at 15-Dec-2020 09:03. So not sure if this really is the issue.