There are many pairs of species which can interbreed, and sometimes be fertile, and as a result genes can get from one to the other. But for the most part they don't interbreed, even when they share a territory. An example today is tigers and lions. (They no longer overlap in the wild, but they used to before humans shrank both their territories.)
Similarly homo sapiens and neanderthals coexisted for tens of thousands of years. And yet we only have evidence for a handful of successful interbreeding events. That's pretty good evidence that they were separate species.
For these new ones, whether they were fertile or not is subject to dispute. However we can estimate how far back the last common ancestor of their chromosomes and ours is. And from that gap, we have reason to believe that they are similarly distant from homo sapiens as Neanderthals were. And so they likely were a different species, even though some interbreeding was possible.