Comment 24 for bug 1359199

I can confirm this still happens.
After an arbitrary amount of time focus follows mouse just stops and fiddling with settings makes no difference. Sometimes a few weeks will pass before it happens. I've not been able to link it to a specific app, but in case it matters I do use KeePass2, which I see mentioned in other posts. Keepass2 is not always running when the bug triggers.
Restarting the desktop via login works, but this is rather annoying.

# cat /etc/linuxmint/info
RELEASE=18
CODENAME=sarah
EDITION="Cinnamon 64-bit"
DESCRIPTION="Linux Mint 18 Sarah"
DESKTOP=Gnome
TOOLKIT=GTK
NEW_FEATURES_URL=http://www.linuxmint.com/rel_sarah_cinnamon_whatsnew.php
RELEASE_NOTES_URL=http://www.linuxmint.com/rel_sarah_cinnamon.php
USER_GUIDE_URL=help:linuxmint
GRUB_TITLE=Linux Mint 18 Cinnamon 64-bit