But I think those are examples of neurons operating normally, not abnormally. Even in the case of mind-influencing drugs, mostly the drugs just affect the brain on its own terms by altering various neurotransmitter levels. On the other hand, a low-level emulation glitch could distort the very rules by which information is processed in the brain.
Note that I am distinguishing "design shortcomings" from "bugs" here.
I don't quite see how you'd get "the overall rules" wrong. I figure standard software engineering is all that's required to make sure that the low-level pieces are put together properly. Possibly this is just a failure of imagination on my part, but I can't think of an example of a defect that is more pervasive than "we got the neuron/axion model wrong." And if you're emulating at the neuron level or below, I'd figure that an emulation shortcoming would look exactly like altering neural behavior.
Reading this article on requiring lots of processing power to emulate the snes accurately, made me think that we will likely have similar issues when emulating humans.
I'd imagine weird timing and chemical interactions being used by the brain as it is an adaptable system and might be able adapt to use them if they turn out to be helpful.
This suggested to me a few issues with no easy answers that I could see.