Hello,
When trying to update from Ubuntu 15.10 to 16.04 beta (not sure the final version is out there yet), the update manager wants to install some packages from Gnome/Unity that are not supposed to be part of Mate. Like Nautilus, some packages related to Gnome online accounts, parts of Unity and Gnome Control Center and so on. I first thought it was an issue on my system but I’ve tried a fresh 15.10 install in a VM and it does the same when upgrading.
Is it a known issue? is it still there when upgrading to Ubuntu Mate 16.04 final?