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That's a great question. Voyager 1 was launched after Voyager 2, but along a shorter and faster trajectory that was designed to provide an optimal flyby of Saturn's moon Titan. So I'm guessing that they were numbered not buy launch sequence, but by target arrival sequence. From Wiki:

The Voyager Program was similar to the Planetary Grand Tour planned during the late 1960s and early 70s. The Grand Tour would take advantage of an alignment of the outer planets discovered by Gary Flandro, an aerospace engineer at the Jet Propulsion Laboratory. This alignment, which occurs once every 175 years, would occur in the late 1970s and make it possible to use gravitational assists to explore Jupiter, Saturn, Uranus, Neptune, and Pluto. The Planetary Grand Tour was to send several pairs of probes to fly by all the outer planets (including Pluto, then still considered a planet) along various trajectories, including Jupiter-Saturn-Pluto and Jupiter-Uranus-Neptune. Limited funding ended the Grand Tour program, but elements were incorporated into the Voyager Program, which fulfilled many of the flyby objectives of the Grand Tour except a visit to Pluto.
Voyager 2 was the first to be launched. Its trajectory was designed to allow flybys of Jupiter, Saturn, Uranus, and Neptune. Voyager 1 was launched after Voyager 2, but along a shorter and faster trajectory that was designed to provide an optimal flyby of Saturn's moon Titan, which was known to be quite large and to possess a dense atmosphere. This encounter sent Voyager 1 out of the plane of the ecliptic, ending its planetary science mission. Had Voyager 1 been unable to perform the Titan flyby, the trajectory of Voyager 2 could have been altered to explore Titan, forgoing any visit to Uranus and Neptune. Voyager 1 was not launched on a trajectory that would have allowed it to continue to Uranus and Neptune, but could have continued from Saturn to Pluto without exploring Titan.