I think this gets reasonably answered in the sequels with the idea that anything strange happening in the Matrix is explained as being something supernatural. I always imagined anyone who saw an agent take over a body and spoke about it would be dismissed by the system and bluepills as them simply seeing things, or some other gaslight equiviliant term designed to supress the truth.

A fun read. I love that we're still poking this facinating movie more than two decades later.