Why does Pluto's Orbit underlap inside of Neptunes Orbit. Clearly Neptunes Orbit is not overlapping on Pluto's. Yet, they fail to maintain the symmetric banding appearance all the other Planets maintain, similar to the quarter mile track you often see around football fields.
There are a few peculiarities of Pluto's orbit. These are:
Its high orbital eccentricity (e = 0.25) causes Pluto's perihelion to be ever so slightly smaller than Neptune's perihelion.
Pluto has an orbital resonance with Neptune. Its orbital period is exactly 3/2 of Neptune's. This orbital resonance is the cause of its orbital eccentricity that you ask about.
Pluto has an orbital inclination of 17 degrees to the ecliptic. No one knows why, we can only guess.
The origin of Pluto's eccentricity explained:
During the later stages of planet formation, in this early Solar system, the planets were still forming. Neptune exchanged angular momentum with the remaining planetesimals, and its orbit expanded outwards. If Pluto were in a near-circular orbit larger than Neptune's (at about 33 AU), there is a high chance that Neptune could capture Pluto and lock it an orbital resonance (this probably happened when Neptune was at about 25 AU). As Neptune's orbit continued to expand outwards, this expansion drew out the eccentricity of Pluto's orbit.
Source and further reading: The Origin of Pluto's Orbit: Implications for the Solar System Beyond Neptune