My take: Red Herring.
Reason - at that time, when metabolic endproducts hit the ventilators CJ was very paranoid herself, because more and more Dunbarians went missing; CJ assumed they went away and thus betrayed her, so she had quite a strong pessimism about anyone - except for Sean.
Another reason why I think Skittles had no reason to let Ink in: Skittles hat no idea about what hell would break loose the moment he allowed Ink to enter. As the audience we learned that Ink appeared "normal", if you looked at him through a camera-system. Paul and Lizzy fell for it; why would this be any different from Skittles/ Duncan? Also keep in mind: If Duncan/ Skittles had kind of a personal connection to William/ Bill, why would he have freaked out after the fall of Dunbar and not tried to get in touch with Ink again? Instead of this he tried to keep as much distance from him and smart ones as possible; Skittles was quite "confident" in claiming Ink to be the worst zomb in LA ...
The only thing I would buy is that Duncan recognized Ink as someone he knew without knowing, though, that Ink was leading a zomb-army. So, if CJ wonders, if Skittles let him in on purpose, then this wuld be true only in the case that Skittles wanted only him in - and not a zombie-horde. No ... Let's keep it simple. For as long as we have no confirmation about any relation between Skit and Ink, as long we are not well adviced to assume too many things. So I keep it as I introduced it: red herring ...
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