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.
People tend to misintrepret what the simulation hypothesis actually suggests. The idea isn’t that these simulated worlds would somehow be fictional or like video games. The point is that we take the known physics of the universe and run computer simulations of it. Things like magic would be just as impossible in these simulations as they are in the base reality. There’s no reason to expect that things would be any different even if we in-fact did live in a simulated world.
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.
There are multiple simulation hypotheses, both are possible, as are others.