Warning about updates after installing Kali linux tools
The LionSec Katoolin GitHub webpage clearly warns Katoolin users to be careful when updating software.
Before updating your system, please remove all Kali-linux repositories to avoid any kind of problem.
All kinds of problems can occur if you don't do this.
Additional reference: How to install Kali linux tools in Ubuntu 15.10
Are the kali repositories necessary?
Katoolin is a script that makes it quick and easy to install may Kali linux tools at the same time, however adding Kali repositories is not always necessary. For example read this answer to a question about how to install only two Kali linux tools, which can also be easily installed without adding Kali repositories.
Adding only the Kali linux tools that you need manually is good training that teaches you how to use the other package management tools that are provided by the default Ubuntu repositories and which are safer than Katoolin because they don't add a long list of additional repositories to your software sources.
If you need to install a lot of Kali linux tools you should also consider installing Kali Linux itself, either as a dual boot or in a virtual machine. If you have done what looks like irreparable damage to your system with Katoolin, I recommend that you remove all the Kali linux repositories that you added from your software sources and with the help of the terminal
history command remove all the packages that you installed with Katoolin, and start over again with vanilla Ubuntu. You should certainly try this before you give up and reinstall Ubuntu.