They have been cleansed by the word (Eph 5:26, James 1:18); actually by the whole of His message to them. He is not rebuking them, but encouraging them. Note that “clean” (katharos) is the same word used in (13:10) which excluded Judas. The branches which are cut off are people like Judas, who had a great deal of contact with Jesus but was never a real disciple.

Ephesians 5:26  to make her holy, cleansing her by the washing with water through the word,

James 1:18  He chose to give us birth through the word of truth, that we might be a kind of firstfruits of all he created.

John 13:10  Jesus answered, “A person who has had a bath needs only to wash his feet; his whole body is clean. And you are clean, though not every one of you.”