My 3 month old baby been prescribed ranitidine 0.53ml 3x day domperidone 1.5 ml 3xday for silent reflux can this medicine cause smelly diarehea?

Very possible: If your baby's feeding and discomfort has improved and the bowel movements have not become excessive, this may be a bit of bowel adjustment to the new overall state of affairs after starting a new selection of medications. These meds change the overall environment in the bowel and may change the consistency and smell of the stool.

See below: Any medicine given orally including medicines that alter gut processes can change the bacteria flora and thus, change the smell of the stool.