From what I have learned and observed for some time now, it seems like any sickness is caused by bacteria, virus, pathogen/parasite, fungi. Which really all can be in the parasite catagory.
It does not have to be worms or something similar, some parasites can't be seen with the naked eye but cause many health issues. Maybe the cleanse stirred up the pathogen, but didn't kill it. If it were me, I would keep cleansing. Not everyone agrees, but I don't believe in the 30 day cleanse, 90 day break.