Hello,
Default Companies and Contact groups are locked in epesi. We applied this feature to prevent the very common occurrence of deleting entries and whole tables from CommonData by admins and then asking for support because they don't know how to manage some entries or epesi starts failing.
But to answer your question - there is currently no option in UI to delete these entries. You can, however, delete Contact Groups directly from the database and it shouldn't cause any harm to your installation, even if any contact was assigned to them.
To help you find these entries, you can use the following query:
SELECT * FROM utils_commondata_tree WHERE parent_id=(SELECT id FROM utils_commondata_tree WHERE akey="Contacts_Groups")
However, I can't recommend the same for Company Groups (or other arrays), since for instance the "Customer" group is used by some of the modules in epesi. Deleting that group will cause these modules to stop operating properly.
If necessary, it's much better to change the value (displayed label) for these groups, leaving the key intact. That way it will still function properly - it's the key that matters for all epesi checks - and you can have any label you like.
Hope this helps.
Kind regards,
Arek