No not the core it's one of the poles, Birkeland currents discharging at the poles.
I believe the same is true on Saturn which recently had it's south pole hot spot confirmed, similar story on Venus, the Earth as well has been confirmed to be receiving charge from the sun via magnetic flux ropes (Birkeland currents) focused at the poles. Sometimes these hotspots are the centre of a vortex as on Saturn and Venus.
All pieces of the solar circuitry.

Originally posted by ziggy1706
Or, could jsut be missing camera info.

Bingo, you win the prize. It's missing info. The shots for this animation were not actually taken looking down at the pole, they were taken with cassini looking at the planet from the side and then re-projected in a computer as if a virtual camera were looking down at the pole. Because there was not complete coverage of jupiter's pole there is a gap in the data and thus a "hole" appears. From NASA's website:

Persistent polar storms and zonal winds on Jupiter can be seen in this magnified quadrant from a movie projecting images from NASA's Cassini spacecraft as if the viewer were looking down at Jupiter's north pole and the planet were flattened.

The sequence covers 70 days, from October 1 to December 9, 2000. Cassini's narrow-angle camera captured the images of Jupiter's atmosphere in the near-infrared region of the spectrum.

Although Cassini did not orbit jupiter it did pass close enough for a good look.