Because E-Verify is still relatively new, is not mandated (Obama tried to get its use mandated, and failed), and several states absolutely forbid its use. And it's notoriously unreliable, in no small part because it relies on an immigration system that's unreliable (I know one story where a naturalized citizen was denied work because after he received his Certificate of Naturalization from USCIS, the State Department failed to inform ICE that he was naturalized, so DHS denied the I-9. How *****-up a bureaucracy is that, that the State Department has to notify DHS of what another DHS branch is doing?)
This story is not nearly as black-and-white as reports make it out to be.