After generations of Zoroarks and Zoruas living as humans with their Illusion ability, the Zoroark we know from our time began to change and adapt to their new preferred way of living.
Feral Zoroarks used to spend years trying to speak the human languages, learning the rules of society and law. Becoming as human as possible was difficult for them and only a very small number succeeded whereas other gave up and moved back into the forests.
As more and more Zoroarks adopted to their new lives, so did the humans around them. After countless failures of their ability to hold their illusion, mostly due to fatigue, stress or illness, humans set up foundations and facilities for burnt out Zoroarks wanting to come to terms with themselves.

As the years rolled on, the Zoroarks began to change. They stood more upright; their vocal chords adapted and even grew additional digits, not to mention their tails returned! Their evolution was incredibly rapid but not totally unexpected being related to Pokemon after all.
Now, in their current form, pokeballs no longer recognise them as being pokemon. Rightly so some would say.