Where do humans come from in the Pokemon Universe, that's a question I haven't thought of. The very original idea about the in-universe origin of Pokemon is that one day they just appeared (okay, not the most complex origin story, they do try filling it out by saying they came from space), but obviously that idea has been long abandoned (at least in the Pokemon universe) with their being ancient Pokemon that predate when humans would have existed. But in that case, if Pokemon predate humans then WE'RE the ones who are the anomaly, not the Pokemon. According to legends (which in the Pokemon universe can be true), everything started in a swirling mass of chaos until an Egg was created and from it hatched Arceus who caused time to flow and space to bend. Arcues is a Pokemon, and he created more Pokemon to control and meld the universe and Pokemon World as well a ones to live upon it an spread. It's a bit foggy what happened from there, the Mew species was made in abundance but they quickly evolved into other species of Pokemon. Then we have the prehistoric era where for millions of years the Fossil Pokemon lived and thrived. All this and still no humans in sight.
Coming to ancient historical times, obviously humans have come into existence as there are manmade artifacts and messages left behind. As
Daemul pointed out, there are a few myths of people and Pokemon being one and the same once. Though these stories are just possible allusions to some real life mythology (they sound similar to stories of swan maidens and selkies), it could also possibly show either humans are indeed an offshoot of the Pokemon species (somehow) or even ancient people wondered this very question and decided to relate themselves to the magical creatures who they probably had the legends where they came from.
But if that's so, how come Arceus is sometimes shown to have a disdain for humans? Are we not still his children? If the "humans were once Pokemon" story was true then there would have to have been an event where the beings we would first consider human having maybe betrayed Arceus or forgone their Pokemon nature (Pokemon Adam & Eve?). But for what purpose would these proto-humans do that? Did they want to be consider special or possibly superior to their Pokemon peers? Did they not want to listen to the likes of Arceus and other powerful Legendaries and instead carve out their own destiny? Or, going off the Adam and Eve idea, were humans an experiment by Arcues which fell through but somehow the proto-humans were able to survive and multiply.
Or, if you don't like the religion aspect of things, if we were to go by a scientific route what would cause either a human split from Pokemon or humans developing independently/parallel to Pokemon. Going with the split idea I guess you can say humans went from being Pokemon how humans went from being animals in real life. Humans gained the intelligence to use tools, create complex social structures, create communities, tame both land and their once fellow Pokemon until they became what we would consider fully human; completely split from their Pokemon side. But humans are pretty different from Pokemon as
MetalKing1417 points out, so could it be possible human development had nothing to do with Pokemon? Well for that to happen then my guess is that, with Pokemon existing, survival of a species different from Pokemon was very difficult. For another species to develop alongside humans they would have to be adept survivors, being able to ignore being easy prey as well as maintaining a sizable population to breed. Obviously it would be very difficult, but life finds a way and the evolution line that eventually became humans was either lucky enough to accomplish this or early on there was some connection between them and Pokemon that was beneficial to the Pokemon. So as time went on eventually the proto-human(s) came into existence and began using their different intelligence from Pokemon to begin the process of becoming modern day humans.
And that's to mention all the mix-and-match things you can do. Like Arcues realizing for Pokemon to become stronger there needs to another species disconnected from them that they can bond with, so started the evolutionary process that'll become humans (that was Pokemon were directly created by Arceus while humans went through the process of evolution how we know of it in the real world). Or maybe, as
MetalKing1417 said, Arceus pulled humans from elsewhere (maybe the reason Hoopa was made?) in the multiverse and THAT'S why to ancient humans it seemed like Pokemon came out of nowhere yet there are fossil Pokemon. Or maybe it wasn't Arceus, maybe it was another kind of cosmic force that maybe caused the Pokemon world and a world with humans to merge into one.
So, what is the answer to where human came from in the Pokemon World? I don't know, TAKE YOUR PICK! Phenomenal or natural? Arceus or no Arceus? From Pokemon or individual? Evolution or transportation? Maybe someone should ask Professor Juniper, with all her studying of Pokemon origin at some point she had to stumble upon some bits or human origin, right?