Something similar is possible in humans due to a difference in Rh blood groups.
The Rh blood group system consists of 49 defined blood group antigens1, among which the five antigens D, C, c, E, and e are the most important.
[A]ntibodies to the Rh(D) and Rh(c) antigens confer significant risk of hemolytic disease of the fetus and newborn.
(from Wikipedia)
In short, the egg and sperm of Rh incompatible people can produce a living fetus, but antibodies of the mother attack the blood cells of the fetus which often leads to the death of the fetus if not treated.
Please note that in humans this mechanism takes effect only after the first pregnancy. The first child is born healthy, but after that most or all pregnancies end in miscarriage or the children dying shortly after birth.
Since you create your own species, you can adjust the mechanism so that even the first child of an incompatible couple dies.
