The 2 minions with Chester Doors are extractable, the problem however is this is not a repeatable quest. I discovered this by running one of my wizards who did not do wysteria yet, then porting into the battle. There is no sigil at this instance either so you can not do team up and hope to meet up with someone with the quest.
To me it makes sense to make this battle repeatable, if not, those creatures need to be removed from the tome. They are the greenman minion and barkskin treant (different than the wandering mob somehow).
I would post pictures but you can not do that here. I get the feeling that some of the other "missing creatures" are from non-repeatable bosses, but unless I run all new wizards to max really no way for me to tell.