Kali Linux Update Problem Repository

Your /etc/sources.list should be:

deb http://http.kali.org/kali kali-rolling main contrib non-free
# For source package access, uncomment the following line
# deb-src http://http.kali.org/kali kali-rolling main contrib non-free

However if the above official source not working to you, you may use the official kali mirrors.
 
1) Go to this link http://http.kali.org/README.mirrorlist
2) under "mirrors which handle this country" copy any one of the link (example in my case: http://kali.cs.nctu.edu.tw/kali/README )
3) Open nano /etc/apt/sources.list and paste it at the bottom.
4) Remove "/README" from the link and make it looks like this -> "deb http://kali.cs.nctu.edu.tw/kali kali-rolling main contrib non-free"
5) Comment all previous sources except the mirror that you just pasted.
6) and finally your Mirror sources.list should be like this: (Example of my kali mirror sources.list)

#Kali Linux Rolling Official Repositories
#deb http://http.kali.org/kali kali-rolling main contrib non-free

#Kali Linux Rolling Official Mirrors Repositories
deb http://kali.cs.nctu.edu.tw/kali kali-rolling main contrib non-free

7) Exit and write changes.
8) Run apt-get clean && apt-get update and see if it works.
9) If it still doesn't working, try to replace it with another mirror.

Hope this helps anyone out there.