Remove the insole of the shoe purporting to be a Prada; on the bottom side, it should read "Prada" at the heel, and it should feature a Prada logo with the words "Made in Italy" beneath the logo. Insoles glued into the shoe and with different logos are fakes.
Prada dress shoes that feature a toggle rather than Velcro straps or laces should feature the word "Prada" in text only one side of the toggle. If the shoes come with a sleeper bag, examine the material. It should be silver plastic and should feature a silver drawstring. Any variations indicate the possibility of a knockoff pair of shoes.
Another important thing to check is the box. A real Prada box only has one logo on the side of the box, in the same place as the pricing information and the shoe model. Prada boxes are made of corrugated plastic, rather than cardboard. If the logo appears on top of the box, chances are that you're dealing with a fake.
One more strategy for identifying fake Pradas is to visit the Prada website and examine the lines for each season. If the shoe you are considering in is not part of any of these lines, it is likely a fake.