Upgrades can be tricky and sometimes you may see output from this tool that you do not expect, either too many or too few things reported.
If you are expecting to see output for somefile.phtml you can run the tool like
php bin/patch-helper.php analyse /path/to/magento2/ --filter "somefile.phtml" -vvv
This will show the file being scanned and whether it is being validated or if it is being skipped. You can use XDEBUG to step into the specific src/Ampersand/PatchHelper/Checks file that you think should be detecting it or raise an issue with the verbose output.
Check to see if your patch file has been generated properly
Running the following command will give you an idea of how many Magento files have been changed in your vendor.patch, if you do not see a lot of entries here it is likely your vendor or vendor_orig directories are not as you expect them to be (perhaps the upgrade failed to be completed properly?)
grep 'diff -ur -N vendor_orig/magento' vendor.patch
Warnings and notices may pop up at the top when some things are not handled properly (for example #103)
You can run the tool like so, which will throw an exception with a trace for any error encountered and verbose mode will let your know the files responsible for the issue.
php bin/patch-helper.php analyse /path/to/magento2/ --php-strict-errors -vvv