The Pluto texture has its reference meridian off by 90 deg, and it is rotated upside-down.
To find the reference meridian Pluto, and the orientation of its latitude and longitude, look at this map ((0, 0) is opposite the heart).
Side note: in this discussion it actually matters that the longitude used on Pluto yields an orientation consistent with the convention on Earth and Mars, and inconsistent with other planets and satellites of planets; happily, since we're only looking at Earth and Pluto below, we can know that it's consistent and forget about it again. For gory details on coordinate systems in planetary astronomy, see Emily Lakdawalla's article on the matter.
Here is the Pluto texture currently in KSP-RO/RSS-Textures, with annotations showing the directions of latitude and longitude, and the reference meridian.

Compare this with the Earth texture: the latter correctly has longitude running right to left, latitude running bottom to top, and the origin of longitude a quarter of the way in from the left.
The biome map is similarly oriented1, so here it is for illustration purposes; I have not found it necessary to annotate the directions of latitude and longitude nor the reference meridian, the outlines of landmasses should be familiar enough.

This wasn't caught, because, due to their inclination, Pluto and Charon cannot be tidally locked in stock. However, in the current (unreleased) state of Principia, which has axial tilt, Charon gets to look tangentially at Pluto's heart (it should not).
Other small solar system bodies may be affected (an incorrect rotation of anything other than the Earth and its moon is hard to spot in-game).
1 The biome map and EarthColor actually differ by a reflection about the equator.
The Pluto texture has its reference meridian off by 90 deg, and it is rotated upside-down.
To find the reference meridian Pluto, and the orientation of its latitude and longitude, look at this map ((0, 0) is opposite the heart).
Side note: in this discussion it actually matters that the longitude used on Pluto yields an orientation consistent with the convention on Earth and Mars, and inconsistent with other planets and satellites of planets; happily, since we're only looking at Earth and Pluto below, we can know that it's consistent and forget about it again. For gory details on coordinate systems in planetary astronomy, see Emily Lakdawalla's article on the matter.
Here is the Pluto texture currently in KSP-RO/RSS-Textures, with annotations showing the directions of latitude and longitude, and the reference meridian.

Compare this with the Earth texture: the latter correctly has longitude running right to left, latitude running bottom to top, and the origin of longitude a quarter of the way in from the left.

The biome map is similarly oriented1, so here it is for illustration purposes; I have not found it necessary to annotate the directions of latitude and longitude nor the reference meridian, the outlines of landmasses should be familiar enough.This wasn't caught, because, due to their inclination, Pluto and Charon cannot be tidally locked in stock. However, in the current (unreleased) state of Principia, which has axial tilt, Charon gets to look tangentially at Pluto's heart (it should not).
Other small solar system bodies may be affected (an incorrect rotation of anything other than the Earth and its moon is hard to spot in-game).
1 The biome map and EarthColor actually differ by a reflection about the equator.