In Chamilo 1 there was the settings show_glossary_in_documents to define if it was not shown or manually selected or automatic.
In Chamilo 2 only the automatic selection has been implemented (manual assignation not needed any more).
To make settings more consistent in Chamilo 3, the documents.show_glossary_in_documents should be removed since it is only automatic, and if we do not want the glossary to be shown we should use the setting "Show the glossary terms in extra tools" (glossary.show_glossary_in_extra_tools) and select the option "None".
Tambien agregar documentos en la lista de herramienta en la cual se puede activar el glossary.