Physically, it could be because the different species have different methods of breeding/giving birth. I don't know what your humanoids are like, but different gestation periods, reproductive systems, rearing methods, and physical biology could play a part.
1. Amphibious nixies mating with humans might try to raise their offspring underwater - and the newborns might be unable to survive without air.
2. Humans are pregnant for 9 months while elves may be pregnant for 2 years. Elven mothers would carry half-human babies for too long, and human mothers would give birth too early to half-elves.
3. Different species may have completely different blood types, resulting in *severe haemolytic disease* and *hydrops fetalis*. For more info on both conditions, see here: https://en.m.wikipedia.org/wiki/Blood_type
4. Some species might be predominantly intersex or hermaphroditic - or, if magical, capable of self-replication and therefore be biologically infertile.
5. Newborns might be fed in different ways. If a vampiric child was born to a human, it would either kill its mother (and then potentially starve to death, as it may only be compatible with its mothers' blood until it matures), or starve earlier as it would refuse to suckle.
On a less physical/biological level, certain cultural differences may be in place. If Group A and Group B live in close proximity, but perhaps distrust each others' cultures enough to make interspecies relationships taboo enough that resources, material goods, and emotional support would be withheld. Few already-weak interspecies babies would survive exile.
If you wanted a different kind of plot point, it could be that interspecies children are too powerful/destructive/etc. An ancient edict may demand that no cross-species child be allowed to exist - and the odd exceptions may set fire to villages/level towns/bring plagues to cities that eventually occasion their death as well.
Biological reasons are probably easier to enforce than social/cultural 'rules' (someone always wants to be different!), but a combination of the two might work as well.