This is a normal - and even healthy - reaction that indicates that parasites, fungi, viruses, bacteria or other pathogens are being effectively killed off. The "additional reading" links below describe the symptoms of "die off" and why it occurs. This is especially true with fungal infestations. When a fungus dies it spews out mycotoxins that make the current symptoms of disease even worse. The cure can only happen after the fact. So it's like an addict ending an addiction. You can't get there without going through the process. This is why when someone starts The Real Diet of Man they may feel ill for a week or two. It's part of the healing process.
For additional reading: