Sometimes usage of the LazySourceIndex when calculating manifests might lead to orphaned items in buckets. This happens because the parent structure of bucket folders is not always processed correctly.
The issue affects Sitecore Publishing Service from 2.2.1 to 4.2.1.
To resolve the issue, consider the following option:
Note: The suggested configuration file makes specific Publishing Service instance always use FullSourceIndex. The default configuration is available at the following path: /sitecore/publishing/sc.publishing.services.xml).