I just tried to reproduce the problem on a clean install of Kali 2.0 on a pendrive and it gives the error the first time "apt-get upgrade" is run, but once I run "apt-get upgrade --fix-missing" the problem doesn't appear anymore.

Just to let you know that a clean install should work as it should, if you really need a copy of Kali running up to date ASAP.

I just tried the same steps again. Downloading from Kali's Download Page And doing a Clean install And I still got the same error. I even tried "apt-get upgrade --fix-missing" like you have sugested but it's still the same.

Please indicate us which mirror your are redirected to...

Send us the output of “curl -sI http://http.kali.org/README”

A more complete log showing which package is supposed to be missing would be nice too.

HTTP/1.1 302 Found
Date: Mon, 23 Nov 2015 13:51:26 GMT
Server: Apache/2.4.10 (Debian)
X-MirrorBrain-Mirror: kali2.mirror.garr.it
X-MirrorBrain-Realm: other
Link: http://http.kali.org/README.meta4; rel=describedby; type="application/metalink4+xml"
Link: http://kali2.mirror.garr.it/mirrors/kali/README; rel=duplicate; pri=1; geo=it
Link: http://kali.mirror.garr.it/mirrors/kali/README; rel=duplicate; pri=2; geo=it
Link: http://archive-3.kali.org/kali/README; rel=duplicate; pri=3; geo=de
Link: http://ftp.halifax.rwth-aachen.de/kali/README; rel=duplicate; pri=4; geo=de
Link: http://ftp.belnet.be/kali/kali/README; rel=duplicate; pri=5; geo=be
Location: http://kali2.mirror.garr.it/mirrors/kali/README
Content-Type: text/html; charset=iso-8859-1

apt-get upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages have been kept back:
openjdk-7-jdk openjdk-7-jre openjdk-7-jre-headless
The following packages will be upgraded:
webshells
1 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
Need to get 14.4 kB of archives.
After this operation, 30.7 kB disk space will be freed.
Do you want to continue? [Y/n] Y
Get:1 http://http.kali.org/kali/ sana/main webshells all 1.1-0kali0 [14.4 kB]
Fetched 141 B in 1s (105 B/s)
E: Failed to fetch http://http.kali.org/kali/pool/main/w/webshells/webshells_1.1-0kali0_all.deb Size mismatch

E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?

In the past, we've seen this happen when theres a proxy + AV solution enabled, which flags the contents of the webshell package as malicious. Please check that this is not happening in your place before we proceed.

I have Kali Installed on a system and since after the installation i haven't used it for anything. Only Just tried to Upgrade then i got the error. And there is no Proxy running or even an AV Installed.
Same with the installation on VBox

I just figured it out. I think it's been block by my ISP provider because i use a VPN service now and it was successfully upgraded

Resolved.