I can chown the files with the correct user and it works. but after a while the files seem to be back with the user ‘root’. When I run system health, this comes up as an error.
Is this a major issue and if so, what would be the step to resolve this?
Most likely your cron user that is running the scheduler commands is being run as root,
When you configure your crons make sure you use the webuser, ie
sudo -u www-data crontabe -e
This will ensure the permissions say appropriate.