N: Ignoring file '50unattended-upgrades.ucf-dist' in directory '/etc/apt/apt.conf.d/' as it has an invalid filename extension

See this explanation of the origin and purpose of .ucf-dist files. This means you can either ignore the notice (that's what the N: prefix stands for) or remove said file.

Before you remove the file, make sure it doesn't contain any packages you might still need. Compare it to the one that is currently active on your system:

diff /etc/apt/apt.conf.d/50unattended-upgrades.ucf-old /etc/apt/apt.conf.d/50unattended-upgrades

If you are sure you don't need anything any more, you can ignore this file or remove it. To remove the file run:

sudo rm /etc/apt/apt.conf.d/50unattended-upgrades.ucf-dist

This also happened to me when I upgraded from 14.04 to 16.04, during upgrade installation I was prompted to choose between the original (modified by me) 50unattended-upgrades file or the original one contained in the package update, I of course chose to keep the former.

After installation the uncalled for file 50unattended-upgrades.ucf-dist was present in my system, after I took a quick glance to check if there was any significant change with the old version of the file, it was plain obvious there wasn't any difference, so I simply deleted it.

Bottom line, you can just get rid of it if you're happy with your current version of 50unattended-upgrades.