It's now widely believed that early Homo sapiens crossbred with Neanderthals. Here's an article speculating on why interbreeding may have happened:Human Hybridization
Offspring from mates of two different species often display "hybrid vigor." This author also suggests (using the example of mules) that a hybrid may have higher intelligence than either ancestral species.
These factors show that interbreeding may bestow advantages on the offspring; however, they don't explain why individuals would be motivated to mate with other-species partners. Mistaken identity? As a last resort when members of their own species aren't available? From positive attraction?
In one of my favorite novels, CLAN OF THE CAVE BEAR, Cro-Magnon (Homo sapiens) child Ayla, adopted by Neanderthals, grows up to bear a Cro-Magnon-Neanderthal baby. Her pregnancy results from rape. Like the rest of the clan, the father of her child considers her ugly, or at least odd-looking, and he rapes her to assert dominance, not from desire. Because human babies are born less developed than Neanderthals, Ayla's adopted people think her infant son is deformed. At birth he can't even hold up his head! As he matures, of course, he outstrips his Neanderthal kinfolk in many ways. (As a child, Tarzan in the original novel fares similarly among the apes, who at first take a dim view of she-ape Kala's adopting a hairless, frail creature that will obviously never be able to care for itself. Burroughs' series, by the way, assumes that his "great apes"—definitely not gorillas, which are shown as lesser animals, so the great apes must be a "missing link"—are related closely enough to human beings to interbreed, as seen in Tarzan's visits to the ruined lost city of Opar.) In later books, Ayla learns that other hybrid children exist, usually conceived by rape of Neanderthal girls by gangs of Cro-Magnon men. She speculates that her son may have to look for a mate among these crossbreeds, since both types of human beings often view "children of mixed spirits" as abominations.
James Tiptree's story "And I Awoke and Found Me Here on the Cold Hill's Side" postulates that human beings have a powerful exogamous drive. We're drawn to exotic partners because, in prehistory, marrying out of the tribe kept the genes circulating. A girl's elopement with a boy from the strange people on the other side of the mountain gave evolutionary benefits to her descendants. In Tiptree's story, this impulse has gone wild and become a liability as human beings traveling among the stars pursue the irresistible attractions of exotic aliens, with whom no fertile mating is possible.
Science fiction teems with fascinating human-alien hybrids, such as Spock. In most cases, the writer and reader simply agree to suspend disbelief in inter-species crossbreeding, with no inconvenient mention of incompatible genes. Larry Niven's well-known essay "Man of Steel, Woman of Kleenex" uses Superman and Lois Lane to highlight how improbable this crossbreeding would be. To make such characters biologically plausible, the author would have to assume the galaxy was purposely "seeded" with life from a single point of origin or perhaps that meteors transported DNA through interstellar space.
Margaret L. CarterCarter's Crypt