My 3 Yr Old Son Has Been Having Bowel Problems.

My 3 yr old son has been having bowel problems. It started several weeks ago with pale gray stools which turned into loose yellowish stool to green liquid. And now a yellowish again. All very foul smelling. Just before he started this he was on antibiotics the end of January. Also a few days prior to the stool problems starting he had very bad vomiting. It was his first time ever really vomiting at all. The Dr ran stool samples and are treating him for a possible infection. But it's not definate. One of the test indicated that there was inflammation in his intestines which can indicate an infection. But its just not sitting well with me. Seems like there's another problem.