When Neo is bringing Trinity back to life, you can clearly see many cuts on Trinity's face, but not long after, when Trinity has left the Matrix, you can see that her face is perfectly normal.
Remember that injuries inside the Matrix are there in the Real World.
This is a little complicated to explain, I guess, but here goes. You don't actually take physical damage from the Matrix into the Real World. Think about it - in the first film, Morpheus gets his arse kicked (Yes, I'm British!) just before getting captured, but once he leaves, he's perfectly fine. The Matrix and the Real World are two different places. I realise that Mouse, from the first one again, gets shot to pieces and in the Real World he coughs up blood, and I would guess that's because his wounds were internal. My explanation for these disappearing cuts would be that Trinity only suffered superficial wounds to the face. It's not like her skin would spontaneously open up is it?
--KMeTG
Right basically the matrix and the real world are obviously two totally different places right so thats explained now remember what morpheos said in the first film "THE BODY CAN NOT LIVE WITHOUT THE MIND" cuts and bruises are reconised by the brain but yet cause NO HARM to the actual brain as when mouse gets shot in the first movie his heart stops as he aas did and SO DOES THE BRAIN like morpheos said "the body can NOT live without the MIND (Brain)" see its quite easy to understand.
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