Possibly related issue... I'm curious if 10.12.3 solved your issue or not.
I'm using OS X Server on a Mac Mini and 2 external USB drives to back up a couple of Macs. Working just great under El Capitan for months. Upgraded the clients (but not the server) to Sierra and within a week, the backup failed. For other reasons, I downgraded to El Capitan and again experienced problem-free backups for several weeks. Around the time 10.12.2 released, I decided to try Sierra again. Once again, I needed to create a new backup from scratch within a week.
I created a new backup, and while I'm having no troubles completing initial backups, eventually the backups fail verification and I must start a new backup (the "To improve reliability, Time Machine must create a new backup for you" error.) The disks check out fine when I check them for errors. I do believe the backups are failing/corrupted, but I don't believe that my hardware is the problem.
For the moment, I'm backing up to 2 different disks so that when one fails verification, I've still got a backup on the other, for each computer, but I'm unable to keep more than ~5 - 7 days of backups going due to the repeated failures. Backups fail on either drive, either client, eventually, always within a week or so.
I upgraded to 10.12.3 the day it released with hopes it would solve this issue but I just had to "create a new backup" for my Macbook Pro. So for anyone experiencing the "To improve reliability..." errors, 10.12.3 is probably not going to fix it for you.
Again, I'm certain this isn't a hardware problem as I'm experiencing it quite regularly under 10.12.2 and 10.12.3 and had previously experienced it with 10.12.1 before downgrading and subsequently having trouble-free backups again. El Capitan works fine with this (supported) configuration and Sierra does not.