Your sentence is not grammatically correct and it is a run-on sentence. You cannot have two complete sentences separated by a comma. It you change your sentence to:
He said this was not an issue, and the real issue is that Mary's mother has too many children. or He said this was not an issue. The real issue is that Mary's mother has too many children. Then it is grammatically correct. The first sentence is grammatically correct, and it is also look nice.