Yeah, someone most likely swapped those heads on there. A less-likely occurrence is that someone may have swapped an EGR manifold onto a non-EGR vehicle. Do you know which your vehicle is supposed to be (by the year/model or underhood sticker)?
Anyway, you can jury rig the manifold to get the EGR to function. It involves drilling and installing some plumbing. The plumbing can reside inside the lifter valley.
Drill into the manifold EGR passage nearest the front of the vehicle.
Drill into the exhaust crossover.
Install tubing between these two holes, and seal it up good. Welding is best, but some other high-temp oil-resistant stuff may work (JB weld or something).
Repeat the steps as above, but between the rear-most EGR passage and the intake plenum.
This will work, as exhaust gases will be metered by the EGR valve from the exhaust crossover to the intake plenum. Be sure and use ported vacuum to operate the EGR (not manifold vacuum).
Beware of the fact that this tube setup is not optimal, as the tubes will tend to clog over time. It should get you through the smog check, though.