Time Machine fails to backup certain files A few months back I did a clean install of Yosemite, followed by restoration of user files via Time Machine. Weeks later, I was horrified to find that several dozen files (seemingly random) were missing post-restore. 

I manually checked for the missing files on the Time Machine backup, and they're not there; they were apparently never backed up, despite having existed on the source disk for years, and residing in folders with other files that were backed up just fine. These files were not on the "exclusions" list in TM; they were just ignored for some strange reason.

Since I'm generally paranoid about backups, I keep multiple TM disks around, as well as a Carbon Copy clone and Backblaze. So I was able to manually restore the missing files. But only because I happened to notice they were missing in the first place. 

Since that experience I have taken to keeping a close eye on TM by occasionally comparing what makes it onto the backup vs what is ignored. Today, 

tmutil compare -n 


shows that yet again, I have a random list of files (different ones) that Time Machine is ignoring. I tried to "touch" each file to update the timestamp, followed by a manual TM run, and they are still ignored.

What would cause Time Machine to leave certain files off of the backup schedule? Is there any way to debug this? At this point I have no faith at all in Time Machine, as a faulty backup is in some ways worse than none at all.
The best way to debug this is with tmutil - since you mentioned using the touch command I'll briefly get others up to speed:


open terminal app
open finder to show the folder with the files in question
type tmutil isexcluded and then drag in the files and/or folders in question


Once you know if an item is excluded, you can programmatically remove exclusion or addexclusion as desired. The Time Machine preference pane also has an options button that allows similar modification of the exclusion rules, but no capacity to see if a file will be excluded or not.

Mac:~ me$ tmutil isexcluded /Users/me/Library/Mobile\ Documents/com\~apple\~CloudDocs/Certificate.pdf 
[Included]  /Users/me/Library/Mobile Documents/com~apple~CloudDocs/Certificate.pdf
Mac:~ me$ tmutil isexcluded /Users/me/Library/Caches/1Password 
[Excluded]  /Users/me/Library/Caches/1Password


Once you're comfortable with whether a file is supposed to be backed up, a tmdiagnose analysis might be required. Either by you, or someone that has done that or via support with Apple.