Whenever you upload a file via File Manager, the ownership of the file will be set to the user.
If you download a file within File Manager that has the ownership permission of user:nobody, for example, it will be replaced by user:user. This can be replicated by downloading the file and then deleting it within File Manger. Once you upload the same file, you will notice that the permission is owned by user:user
Where user, is the name of the cPanel account.
For reference, the case number is CPANEL-33598. Follow this article to receive an email notification when a solution is published in the product.
The current workaround is to change the ownership of the file manually.
For example, you will want to type the following to change the ownership for a file named test_file to domain:nobody:
# cd /home/domain/public_html/
# chown domain:nobody test_file