Time Machine fails to backup certain files
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.