Time machine creating files and directories at random places
This seems harmless to me. If you want to clean things up, I would sudo tmutil disablelocal to clean up any local snapshots and then make a new test user and turn off automatic user log in.

Reboot and log in as test and make a clean backup interval without your user being logged in or any files open from the main ~ directory.

At that point, you can check for any odd files or delete them entirely (sudo -s from the test user to become root and able to delete things in your normal user folder).

Again, I don't think any of this will cause issues, but it might be nice to clean things up as described and have a known good backup interval where all files are properly closed and backed up once. Handling files that are always open or always changing is hard for backup tools - so excluding them by rule is also an option.

tmutil isexcluded

tmutil addexclusion file1 file2