My doctor says the same thing - that probiotics are known to aggravate SIBO. But couldn't it also be the case with candida overgrowth (SIFO)?
Dr. Kresser recommends getting a Genova Diagnostics stool test to confirm if it's candida. Mine was done a few months ago and showed no yeast overgrowth (but did show dysbiosis and some bacteria completely absent - like Lactobacillus and E coli). Interestingly, Dr. Jill Carnahan says that stool test may not show candida in the small intestine and that organic acids urine test needs to be done to confirm. My doctor says that some candida would have shown up in the stool test if I had it and she didn't order the urine test. Basically very conflicting information. I tried searching direct labs for Genova Organic Acids test to order myself but they don't seem to offer it.
Interestingly, when I took those probiotics - my skin cleared up of fungal spots (tinea vercicolor) that I have. They're now back though. Xifaxan also didn't help at all - only made things worse. That in addition to all the symptoms that people list here on CZ makes me think it's candida and not SIBO.