I create a message type for comment action with 2 reference entity (field_message_comment & field_message_content), the problem is if the comment is deleted, the message will not be deleted automatically, the message is still there with the token like [message:field-message-comment:body].

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Issue summary:View changes
Status:Active» Closed (works as designed)

you will have to add a rule/ hook that deletes associated messages of the entity beeing deleted, this is not covered by default.