Choice D tells us that the gravitational pull of Pluto is not the sole cause of Neptune's irregular orbit. This does not necessarily mean that it is a a cause at all. In other words, I could say that my praying for rain is not the sole cause of the rain storm. That statement could mean that it's not the only cause, but could also mean that it's not a cause at all.
In any case, though, choice D is correct here because it was originally thought that Neptune's orbit was caused by the the gravitational pull exerted on it by Pluto. We then learned that Pluto is too small to exert that kind of pull. Yet, Neptune is still orbiting. If Neptune is still orbiting, and Pluto is too small to be exerting the kind of pull necessary to cause the orbit, then there must be some other contributing cause to Neptune's orbit, which is what choice D tells us.