There are a number of explanations that insist that the Pioneer effect is really just real deceleration that scientists didn't account for in their predictions. Some of these have merit, some don't.
That there might be other gravitational influences on the spacecraft that we did not consider or know about, perhaps an undiscovered pocket of dark matter or a hefty new planet, is a common explanation. However, seeing that other far-off objects, such as the outer planets, do not seem to be under the influence of any mysterious, unknown gravitational forces, this theory seems unlikely.
Deceleration from drag by the interplanetary medium is another proposal. However, the measured density of this dust, solar wind, cosmic rays and the like is simply too small to make as big of an effect as the discrepancies require.
Drag from radiation pressure is a similar explanation—and one that is also too small to account for much of the Pioneer anomaly. The pressure of sunlight is simply too small at so great a distance. However, some estimates have suggested that as much as a third of the Pioneer anomaly might be due to radiation pressure and heating.