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Hello from JustAnswer.
When a doctor says this, it does not mean that your heart is located in your stomach and beating, but that the heart beat can be seen when looking in the stomach. This is normal.
The heart is inside a firm sac, and this sac is attached to the diaphragm. So, the diaphragm will move in time with the beating of the heart, and this can cause a pressure wave that can be transmitted to the structures immediately below the diaphragm, such as the stomach.
If you are having pain in the stomach, this finding would not be a cause of the pain.
If I can provide any additional information, please let me know.