I don't know if it was problem before or is just a beta thing.
When I run apt update it downloads package list as normal. If I run it again it will download the lists all over again even though there were no updates to packages.
It will download couple of MBs (around 50 megs I think) and on my poor connection will take couple of minutes every time.
Is that a bug on my end? Or on apt?
I updated 15.10 to 16.04.
Solved! It was Virtualbox ppa acting up. Nothing wrong with official repos or apt!