In a nutshell, their efficiency can be questionable.

In 1995 there was a flea product revolution, the market for flea products changed from being primarily over-the-counter to primarily directly through veterinarians. The pharmaceutical companies like this arrangement since their products are now being marketed by trained personnel who can explain best how the product should be used or not used. Over-the-counter products out in stores these days often rely on insecticides that have been out long before the ones prescribed by your veterinarian, and resistance among the flea population can be pretty significant. In addition, these products often lack residual effects, giving a chance for the flea population to sprout back up again immediately. They can also have rather harsh toxic effects if not used properly, such as muscle tremors or even seizures. Products prescribed by your veterinarian have been scientifically proven to be still effective currently, and if used properly are even safe enough to treat pregnant animals.

Using products as prescribed by your veterinarian can ensure an efficient safe removal as well as prevention of any flea related problems with your pets.