The "fields"? *very minor revos spoilers*
They say in revos that no one has come within however-many (1000?) KM of the machine city. They say in Reloaded, I do believe, that they haven't been to the surface in a very long time if at all. Now, how could Morpheus have "seen the fields with his own eyes" where humans are "grown" and hardwired to the matrix if this is true? (Unless, of course, the "fields" are no where near the machine HQ, and possibly underground if what i'm remembering is correct, which doesn't make sense to me.)
Which leads us on to a 2nd point...how in hell do they "unhook" people from the matrix anyway? Why wouldn't the machines just put a stop to this, I don't imagine it would be very difficult.
Sorry if this is obvious stuff that's been discussed before.