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.
Your point doesn’t necessarily disagree with the OP point. OP is saying that the simulation was supposed to be realistic but had glitches that people interpreted as magic.