Probiotics doing more harm than good?

So after our lo's 2 month apt, her pediatrician told us to start her on probiotics, that theyd make her poop (she pooped fine already) and that they are said to cure any form of colic. So we bought the Culturelle Baby probiotics and had my fiance give her them in her daily bottle. We did this everyday for probably 3 weeks. During this, she was EXTREMELY cranky. She started screaming as if in pain, wiggled horridly and would cry as she'd wiggle her little farts out... i literally held her and rocked her all day every day, even taking off work, and i only work 3 days a week. So finally after tons of diet adjustments to see if that caused it, we narrowed it down to the fact she starts acting up after her bottle usually. It had been days since she had pooped and thats not normal. Shes usually at LEAST a once a day pooper. My fiance decided to not use the probiotics one night and BAM she was happy, content and fine ALL NIGHT. We stopped them completely and since shes been a totally different baby. She farts easily, is eating better, has been pooping every day again. I searched and found multiple forums and threads of mamas bringing their baby to the er from such horrible tummy problems and having miserable babies. Has anyone else had a bad experience with probiotics? Our lo is ebf as well.