First, the Wachowskis themselves directly say to their fans while chatting with them that the mirror is Neo's hallucination:
ThedrickFel: What exactly was the mirror made of? Was it the same stuff they injected into Morpheus? Why silver?
WachowskiBros: The mirror is actually a mirror. When Neo sees it, it's a hallucination, but it's the direct result of the pill Morpheus has given Neo. Reflections in general are a significant theme in the film. The ideas of worlds within worlds..
The mirror itself is not doing anything - this is all purely due to the red pill program that is disrupting Neo's I/O (input/output) signals. What exactly are Neo's I/O signals? His five senses, of course! More specifically, the disruption of one of Neo's input signals (vision) causes Neo to hallucinate a mirror, while the disruption of a couple of Neo's output signals (vision, touch) cause Neo to change his own reality by imagining that the mirror is taking over his own body.
While Morpheus and Trinity wouldn't be able to see the effects of Neo's disrupted input signals (they can't see what Neo sees), Morpheus and Trinity would certainly be able to see th effects of Neo's disrupted output signals (what Neo imposes into his world through belief). That is why Morpheus and Trinity could see this strange liquid replicating itself over Neo's body, but also why neither Morpheus nor Trinity commented on the mirror Neo saw when it first changed shape. Morpheus probably figured out that Neo was hallucinating, however, since hallucination would probably be inevitable for someone who just took the red pill.
The scene is purposely designed to be strange. Remember that Morpheus tells Neo that he will see "how deep the rabbit hole goes," and Cypher told Neo to "buckle your seatbelt, Dorothy, because Kansas is going bye-bye." These two references to Alice in Wonderland and The Wizard of Oz are probably the best examples the Wachowskis could have picked to hint at the strange things Neo was about to experience in his journey to the real world. But amazingly, the red pill and its i/o signal disruption capability still keep this brief scene of "weird fantasy" grounded in firm science fiction.
With this scene, I feel that the Wachowskis are telling us, "You know how weird The Wizard of Oz and Alice and Wonderland are when Dorothy's house gets picked up by the tornado and when Alice tumbles down the hole? They require the total suspension of belief. Well, we're going to give you a scene that is equally weird as those scenes, except we won't require you to suspend belief. It will make absolutely perfect sense within the realm of science fiction. What? You say it's impossible? Watch us."
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