Duplicate entities means that they have same 'name', 'default value' and 'help message'.
Current generator can not deal with the duplicate entities in different groups. They will be added into the same group in tempest.conf.sample. As generator compares opt with the opts in groups to find the group in which the opt is, duplicate opts will be matched in the same group.
For example:
[network-feature-enabled] has 3 api_extensions in tempest.conf.sample. 2 of them should belong to [compute_features_group] and [volume_feature_group]. I reported a bug https://bugs.launchpad.net/tempest/+bug/1280085, and submit a patch making the dup entities different to fix it. But that's not the root cause.
This isn't a tempest bug, the sample generator is synced from oslo-incubator. This needs to be fixed in oslo then we can just update the copy in the tempest repo.