Sometimes, there will be a symbolic, allegorical, philosophical, etc. point, illustration, image, or moment too good for the Wachowskis to pass up even at the cost of strictly rational thinking. The normal rules get overridden by such an element.
Evidence
A good example is the apple in the UN scene of Second Renaissance. Another potential example is Neo's resurrection.
Objections
1. Who says you can't explain it? Apologetics can be given for everything, of course, but we are comparing the probability of that explanation against the strength of the symbolism.
2. Isn't this a slippery slope? Could be. It is pretty subjective to decide what has a plausible rational basis aside from just its symbolic value. Again, here we take the weight and the difference between the obvious symbol and the more vague rational meaning.