Do we get a shot of the computer in the manga?
Watching the scene again, it's very understandable that one would assume the text is speaking of #13. The shot pans over to the three pods for the older androids, and later we see the computer interacting with the androids. However, the narrator specifies a singular entity, even whilst showing three pods, so that doesn't make too much sense at that point in time. The scene could've simply been introducing the ominous new threat, while simultaneously referencing Cell's impending arrival. It may have been trying to do too much at once, which could have gone over the heads of some.