Understanding ner.batch-train stats

If you run ner.batch train with the --no-missing flag, then yes. All tokens that are not part of an entity will be assumed to be not part of an entity. Otherwise, non-marked tokens will be treated as missing values.

The recipe / interface lets you assign labels to text – what they mean is up to you. So you could use the "reject" action to create negative examples, or to mark examples with fundamental problems, like wrong tokenization. Also see this thread: