Scene 2.2: Box 4 contains the scrap tokens, but the new phantom raider rules introduced by log entry 12 do not mention that you would pick up a scrap token each time you kill a phantom raider.
I saw that there is an errate for the Abandoned rulebook on page 21 (where this rule was missing). Is it missing in the log book, too?
no it is not missing. We are giving you the tokens at the same time as the Phantom Raiders (plus it is easier to fit tokens in a box rather than in an envelope), but given the fact that the Raiders actually appear at the end of the scene, there is not much time to do anything with them in that Scene.
So, you will first use these Tokens in the next scene.