I recently ran into the same problem on my OnePlus One in combination Nethunter 3.0.
Tried a bunch of different alternatives that did not play well. In the end I ended up installing a clean CM12.1-YOG4PAS3JL and rooted. After this I flashed NH 3.0, updated the Nethunter App to 3.15 and changed to rolling with the following sources.list.
deb
http://http.kali.org/kali kali-rolling main contrib non-free
deb-src
http://http.kali.org/kali kali-rolling main contrib non-free
Now I could run
apt-get update && apt-get upgrade from the Kali Terminal with no problem.
So, I thought everything was fine and checked the
kali-linux-wireless metapackage from the Nethunter App and hit install/update – Big mistake!
Everything was fine with the installation of the tools but after this the
apt-get update && apt-get upgrade did not work anymore and I was stuck with the “temporary failure resolving…” message
This forced me to roll back and flash NH 3.0 again. This time I skipped the
kali-linux-wireless installation from the App and just ran
apt-get update && apt-get upgrade from the terminal which again worked great.
The current status is that the OnePlus One is up and running and I can use
apt-get for installs and updates/upgrades.