Wasn't the presence of a Pluto-like body _known_ because the orbits of other planets didn't match expectations based on the gravitational pulls of all the other known bodies in our solar system?
Not exactly. It's true that Neptune was discovered that way and that people found Pluto while looking for a "Planet X" that would explain other gravitational discrepancies:
In the 1840s, Urbain Le Verrier used Newtonian mechanics to predict the position of the then-undiscovered planet Neptune after analyzing perturbations in the orbit of Uranus. Subsequent observations of Neptune in the late 19th century led astronomers to speculate that Uranus's orbit was being disturbed by another planet besides Neptune.[1]
However it turned out that Pluto was not Planet X after all. After all Neptune and Uranus are respectively about 7900 and 6700 times more massive than Pluto.
In 1978, the discovery of Pluto's moon Charon allowed the measurement of Pluto's mass for the first time: roughly 0.2% that of Earth, and far too small to account for the discrepancies in the orbit of Uranus. Subsequent searches for an alternative Planet X, notably by Robert Sutton Harrington, failed. In 1992, Myles Standish used data from Voyager 2's flyby of Neptune in 1989, which had revised the estimates of Neptune's mass downward by 0.5%—an amount comparable to the mass of Mars—to recalculate its gravitational effect on Uranus. With the new figures added in, the discrepancies, and with them the need for a Planet X, vanished. Today, the majority of scientists agree that Planet X, as Lowell defined it, does not exist. Lowell had made a prediction of Planet X's orbit and position in 1915 that was fairly close to Pluto's actual orbit and its position at that time; Ernest W. Brown concluded soon after Pluto's discovery that this was a coincidence, a view still held today.[2]
