Since the functions of the digestive system during pregnancy slows down, the amount of stomach acid increases leading to dyspepsia. This digestive system disorder can be followed by other stomach ailments like constipation, heartburn, acid reflux disease (or GERD) and gas (also referred to as flatulence). Another reason is an increase in the Human Chorionic Gonadotropin (hCG) hormone in the system. Nausea also triggers an upset stomach, and it can be a very annoying condition.