When a world is generated or loaded, stray chunks are being generated at the wrong coordinates. This is seen as stray region files with unexpectedly large coordinates. These stray chunks appear to have coordinates that are 16 times what is expected. The terrain at these chunks appears to be the correct terrain for that location - but the chunk itself should not be generating.

This is fairly easy to reproduce because the stray chunks seem to appear fairly consistently in the same locations. For example, create a world with the seed -7374548781075652015. This will generate region files r.0.0.mca and r-1.0.mca as expected, but it will also generate stray region files r.5.13.mca and r.6.8.mca. These stray region files will have single chunks in them at 2560, 6656 and 3072, 4352. Note that these coordinates are all multiples of 256. This suggests that chunk coordinates are being multiplied by 16 twice.

Moving around will sometimes generate additional stray region files, again at fairly predictable coordinates. Movement can be by walking or teleporting; it seems to make no difference.

Code analysis by pokechu22 in this comment.