There is definitely no side effects from taking the 2 together...in my opinion, only a good GI would encourage their patients to find a good probiotic since research has already proven it's benefits with IBD....
Probiotics are nothing more then good bacteria, the only thing that interferes with probiotics is antibiotics because antibiotics kill everything, good and bad bacteria...which is why it's extreamly important that when ever on antibiotics the probiotics are taken at least 2 hours AFTER antis are taken for the day.
The one I use is called primadophilus reuteri made by natures way and it also aids with high cholesterol, lactose intolerance and for women, vaginal health...even if one doesn't have any of the above mentioned issues it's still perfectly fine to take, especially since it does have guaranteed intestinal release which is key when dealing with IBD.
My bum is broken....there's a big crack down the middle of it! LOL :)