I run an Ubuntu Server 12.04.3 LTS. Today, I wanted to update it, but I did not managed it (yes...), however upgrading worked well. I don't want you to solve my problem but it would be greatful if you could give me some hints. I googled hours, I fould a lot of this kind of errors, but not exactly this.

Here is the output of apt-get update:

Hit http://filepile.fastit.net precise Release.gpg
Hit http://filepile.fastit.net precise Release
Hit http://filepile.fastit.net precise/main amd64 Packages
Hit http://filepile.fastit.net precise/restricted amd64 Packages
Hit http://filepile.fastit.net precise/universe amd64 Packages
Hit http://filepile.fastit.net precise/multiverse amd64 Packages
Hit http://filepile.fastit.net precise/main i386 Packages
Hit http://filepile.fastit.net precise/restricted i386 Packages
Hit http://filepile.fastit.net precise/universe i386 Packages
Hit http://filepile.fastit.net precise/multiverse i386 Packages
Ign http://filepile.fastit.net precise/main TranslationIndex
Ign http://filepile.fastit.net precise/multiverse TranslationIndex
Ign http://filepile.fastit.net precise/restricted TranslationIndex
Ign http://filepile.fastit.net precise/universe TranslationIndex
Ign http://filepile.fastit.net precise/main Translation-en_GB
Ign http://filepile.fastit.net precise/main Translation-en
Ign http://filepile.fastit.net precise/main Translation-en_GB.UTF-8
Hit http://archive.canonical.com precise Release.gpg
Ign http://filepile.fastit.net precise/multiverse Translation-en_GB
Ign http://filepile.fastit.net precise/multiverse Translation-en
Ign http://filepile.fastit.net precise/multiverse Translation-en_GB.UTF-8
Ign http://filepile.fastit.net precise/restricted Translation-en_GB
Ign http://filepile.fastit.net precise/restricted Translation-en
Ign http://filepile.fastit.net precise/restricted Translation-en_GB.UTF-8
Ign http://filepile.fastit.net precise/universe Translation-en_GB
Ign http://filepile.fastit.net precise/universe Translation-en
Ign http://filepile.fastit.net precise/universe Translation-en_GB.UTF-8
Hit http://archive.ubuntu.com precise Release.gpg
Hit http://archive.canonical.com precise Release
Hit http://archive.ubuntu.com precise Release
Hit http://archive.ubuntu.com precise/main Sources
Hit http://archive.ubuntu.com precise/restricted Sources
Hit http://archive.ubuntu.com precise/main i386 Packages
Hit http://archive.ubuntu.com precise/restricted i386 Packages
Hit http://archive.ubuntu.com precise/multiverse i386 Packages
Hit http://archive.ubuntu.com precise/main TranslationIndex
Hit http://archive.ubuntu.com precise/multiverse TranslationIndex
Hit http://archive.ubuntu.com precise/restricted TranslationIndex
Hit http://archive.ubuntu.com precise/main Translation-en_GB
Hit http://archive.ubuntu.com precise/main Translation-en
Hit http://archive.ubuntu.com precise/multiverse Translation-en_GB
Hit http://archive.ubuntu.com precise/multiverse Translation-en
Hit http://archive.ubuntu.com precise/restricted Translation-en_GB
Hit http://archive.ubuntu.com precise/restricted Translation-en
Hit http://fr.archive.ubuntu.com precise-security Release.gpg
Hit http://fr.archive.ubuntu.com precise-updates Release.gpg
Hit http://fr.archive.ubuntu.com precise-security Release
Hit http://fr.archive.ubuntu.com precise-updates Release
Hit http://fr.archive.ubuntu.com precise-security/main amd64 Packages
Hit http://fr.archive.ubuntu.com precise-security/restricted amd64 Packages
Hit http://fr.archive.ubuntu.com precise-security/universe amd64 Packages
Hit http://fr.archive.ubuntu.com precise-security/multiverse amd64 Packages
:W: Failed to fetch http://archive.canonical.com/dists/precise/Release  Unable to find expected entry 'main/binary-amd64/Packages' in Release file (Wrong sources.list entry or malformed file)

E: Some index files failed to download. They have been ignored, or old ones used instead.
Hit http://fr.archive.ubuntu.com precise-security/main i386 Packages
Hit http://fr.archive.ubuntu.com precise-security/restricted i386 Packages
Hit http://fr.archive.ubuntu.com precise-security/universe i386 Packages
Hit http://fr.archive.ubuntu.com precise-security/multiverse i386 Packages
Hit http://fr.archive.ubuntu.com precise-security/main TranslationIndex
Hit http://fr.archive.ubuntu.com precise-security/multiverse TranslationIndex
Hit http://fr.archive.ubuntu.com precise-security/restricted TranslationIndex
Hit http://fr.archive.ubuntu.com precise-security/universe TranslationIndex
Hit http://fr.archive.ubuntu.com precise-updates/main amd64 Packages
Hit http://fr.archive.ubuntu.com precise-updates/restricted amd64 Packages
Hit http://fr.archive.ubuntu.com precise-updates/universe amd64 Packages
Hit http://fr.archive.ubuntu.com precise-updates/multiverse amd64 Packages
Hit http://fr.archive.ubuntu.com precise-updates/main i386 Packages
Hit http://fr.archive.ubuntu.com precise-updates/restricted i386 Packages
Hit http://fr.archive.ubuntu.com precise-updates/universe i386 Packages
Hit http://fr.archive.ubuntu.com precise-updates/multiverse i386 Packages
Hit http://fr.archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://fr.archive.ubuntu.com precise-updates/multiverse TranslationIndex
Hit http://fr.archive.ubuntu.com precise-updates/restricted TranslationIndex
Hit http://fr.archive.ubuntu.com precise-updates/universe TranslationIndex
Hit http://fr.archive.ubuntu.com precise-security/main Translation-en
Hit http://fr.archive.ubuntu.com precise-security/multiverse Translation-en
Hit http://fr.archive.ubuntu.com precise-security/restricted Translation-en
Hit http://fr.archive.ubuntu.com precise-security/universe Translation-en
Hit http://fr.archive.ubuntu.com precise-updates/main Translation-en_GB
Hit http://fr.archive.ubuntu.com precise-updates/main Translation-en
Hit http://fr.archive.ubuntu.com precise-updates/multiverse Translation-en_GB
Hit http://fr.archive.ubuntu.com precise-updates/multiverse Translation-en
Hit http://fr.archive.ubuntu.com precise-updates/restricted Translation-en_GB
Hit http://fr.archive.ubuntu.com precise-updates/restricted Translation-en
Hit http://fr.archive.ubuntu.com precise-updates/universe Translation-en_GB
Hit http://fr.archive.ubuntu.com precise-updates/universe Translation-en

And here is my /etc/apt/sources.list:

###### Ubuntu Main Repos
deb http://filepile.fastit.net/ubuntu/ precise main restricted universe multiverse
# deb http://de.archive.ubuntu.com/ubuntu/ precise main restricted universe multiverse
deb http://archive.canonical.com/ precise main restricted universe multiverse

###### Ubuntu Update Repos
deb http://fr.archive.ubuntu.com/ubuntu/ precise-security main restricted universe multiverse
deb http://fr.archive.ubuntu.com/ubuntu/ precise-updates main restricted universe multiverse
deb http://archive.ubuntu.com/ubuntu/ precise main restricted multiverse
deb-src http://archive.ubuntu.com/ubuntu precise main restricted multiverse

Thanks for your help!