MITK point sets contain two point containers, one for ITK, one for VTK points. The size of the two maps can become different after a remove operation.
Cause:
After the removal a new point is selected, but the ID of these new point is chosen incorrectly. The default is the '0' index, the fall back value is (size - 1). However, the points are stored in a map, not in a vector, and possibly no point may belong to the given index. So, when the 'selected' property is set for the chosen element, it can actually overwrite an already deleted item, including its ID.
Secondly, the VTK mapper checked if the point set is not empty and its state is consistent (i.e. the size of the point containers are equal). If these conditions did not fulfill, the function returned.
I had to remove the 'empty' check so that you can remove the last point from a point set from the screen. As I see, in the latest master the visibility is turned off before return, so this change might not be necessary. With 2013.09 it was.
I will send a pull request through github.