Yes...that happened to me when I took Berberine. I felt really good after a week, but the symptoms returned when I stopped taking it because I was not actually in the clear.
Some people do a Colon Cleanse after the antifungals to make sure dead candida is all flushed out. (I did) Also... you can have a stool test ran after treatment to see if its all gone, that is if there is any doubt.