I have just recently updated kali, but before the recent updates about couple days ago. Setting a Mac in Macchanger worked now it doesn't.

Also I did bring the interface down through Ifconfig down command and brought the interface back up after I ran macchanger.

I still have not found a resolution for this issue. I am still wondering if I am doing something wrong or if this is a bug?

Same issue here on an HP ProBook with an Atheros Chipset. Injection, Monitor, everything else works correctly.

Same issue here tho. Reported it. Asus G751JY. Last working version I know of is 1.5.0-9. Can't downgrade it with

sudo apt-get -t=<target release> install <package-name>
nor
sudo apt-get install <package-name>=<package-version-number>

I haven't looked into this problem myself to find a resolution that I could come up with, I been working on other things. Since issue has not been resolved I am taking this over to the forums to begin a discussion there to find a resolution to this problem or if I can find a resolution then I note it here.

The bug is reported here on Debian side:
https://bugs.debian.org/807429

It seems to be that network-manager is resetting the mac interface. But if that's true it does not make sense that macchanger 1.5.0-9 works any better...

You can find older versions here: http://snapshot.debian.org/binary/macchanger/
Please confirm that the problem remains even with an older version...

I fixed network-manager 1.2.2-2kali1 to not reset the MAC address when establishing the connection.

The mac address is still reset when the Wifi connection is brought down but this is a minor problem as you are no longer using the connection at that point.

The development version of NetworkManager has many improvements in the way it handles the MAC address so this will need to be revisited when this new version hits Debian (Testing).