FYI guys, in 3.1 the $many_many and $belongs_many_many relations can not be created/edited by default in the CMS.
One needs to remove the fields by name (luckilly, I do not need to edit or view those relations in the CMS) in order to edit the DataObject.
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Sounds like a bug in DataObject's scaffolding form fields. Should default to a GridField instance.