Lately when I lie down I get nausea and a stomach ache only at night. I also have gained a few pounds. Pregnancy was negative. Help please!?

Heartburn. Certainly this could be a type of heartburn. Adjust your diet, small meals, no chocolate or tomatoes or oil/fatty foods after 5 pm. Also, must se your doctor.
Reflux? A common cause of stomach pain and nausea when lying down is reflux. If acid splashes up from the stomach, these are common complaints. Try some tums, (calcium carbonate) but also schedule an appointment with your doc to be sure.