As I recently outlined in my answer to this question, writing
Magen Darm is wrong according to the German spelling rules. It should be Magendarm.
Magendarmgrippe is a colloquial term for what doctors would call Gastroenteritis — an umbrella term for a number of infections that cause vomiting and/or diarrhoea. It has nothing to do with influenza, even though the same root Grippe is used. Colloquially, it is common to drop Grippe and just speak of Magendarm.
While I myself am not trained in medicine and thus don’t know what a doctor would actually call Gastroenteritis, I would assume that colloquial usage of Magendarm(grippe) is broader than the original term. It is typically already used for severe unwellness that one attributes to the intestinal tract; whether an infection is the cause or not.
So what your friend wanted to say is that she is unwell, probably vomiting or suffering from diarrhoea.