This bug caused T9727. The problem is the equal method of mitkVector.h. There the condition diff.squared_magnitude() < mitk::eps is checked, even for quaternions (or other vectors). This means that if for example the difference of all components of a quaternion is 0.001 the methods returns true because 0.001^2+0.001^2+0.001^2+0.001^2=0.000004 < mitk::eps.
This means the vectors [0.001,0.001,0.001,0.001] and [0,0,0,0] are deemed to be equal at a moment.
Perhaps it's a solution to use sqrt(diff.squared_magnitude()) < mitk::eps. But further discussion is required how to handle equality of vectors.