I looked into the mitkSetRegionTool-class and found the following:

The main work seems to be done with the use of the itkBinaryFillholeImageFilter

• this filter fills holes inside of a given input image
• the input image is the working image with a region growing filter applied to it

This means:

• the region growing filter (ConnectedThresholdImageFilter) fills the selected region using the seed
  • the seed was at the backgrounds so it's 0
  • the bounding contour has value 1 so it's not filled by the region grower

-> we get only the selected region filled with 1's

• now the BinaryFillholeImageFilter continues with this region grower output and fills remaining holes
  • since the new region is now connected with the other regions, any small area encompassed by the selected area is a hole

I created intermediate output images to show the results of the filters:

• the region rowing filter output images looks fine
  • depending on the region I clicked I get a simple contour representing the borders of the clicked background region with 0's outsize and 1's inside
• the binary fill hole filter output image looks incorrect
  • regardless of the region I clicked I always get a single contour (no "concentric contour"), which always encompasses the inner region completely
  • this is probably the desired result for a "fill hole" filter but in this case it's problematic

• It seems as if the ImageToContourModelFilter simply transforms the binary output image to a contour, so it does not modify the contour after the previous filters.

So naively it would make sense to remove the BinaryFillholeImageFilter and simply rely on the connected regions of the region grower.
I removed the fillhole filter and looked at the intermediate filter image outputs:

• the region rowing filter output images looks fine
  • nothing changed here since the region growing filter is the first that is applied
• the image to contour model filter output images looks incorrect
  • regardless of the region I clicked I always get a single contour (no "concentric contour"), which always encompasses the inner region completely

So it seems as if the problem actually lies somewhere in the ImageToContourModelFilter (and the BinaryFillholeImageFilter, but first we need to take care of the former).

The itk description of the itk::ContourExtractor2DImageFilter, which is used inside the ImageToContourModelFilter::Itk2DContourExtraction-function says:

Outputs are not guaranteed to be closed paths: contours which intersect the
 * image edge will be left open. All other paths will be closed. (The
 * closedness of a path can be tested by checking whether the beginning point
 * is the same as the end point.)