Lightning and aurorae are common on Jupiter from probe observations, but no one has ever seen either from Earth, they are much fainter. The last cometary impact (there's been one since Shoemaker) kicked up dark colored material from lower in the atmosphere that was visible for a while after impact, but I don't know if this is a comparable event. I guess we can't rule out a totally different phenomenon, but if that's the case, nothing like it has ever been seen before.

My best guess is a single body small enough that tidal forces didn't cause it to break up before it hit the atmosphere, so it made a single "splash" as it went in, and it was either small enough that it didn't stir up material from below, or the material was there but not visible from earth, or the stain didn't survive a full rotation of the planet.

The impact was near the limb, but I don't know if the impact site was rising or setting, it depends on the optical system he was using, whether it rotated or flipped the image.