Magic may well have been real. Healing crystals, shamanry, witchcraft, voodoo, things of this nature may have been real at one point and have since been patched out. These could have simply been glitches in the program.
We’ve all heard of glitches in games that can be exploited that eventually get patched. Could have been real.
The second Matrix movie basically had this idea in it. Those ghost twins were part of it, but they also straight up mention vampires and werewolves casually as the French dude explained how these all used to be systems setup by the machines to control the system, like a precursor to Agents.
I could imagine that “daemons” may have manifested as actual demons inside the Matrix.