The manipulator is visually in the wrong place in space when having a SubSurf modifier, and enabling it to be Applied on Edit Cage while in Edit Mode.
The mesh and vertices gets applied to editing cage, but the manipulator is still in wrong place _
Attaching two images of it.
correct : manipulator is where selected vertex is
faulty : reading vertex position as editing cage isn't modified. but it is.
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Actually, it's not a bug -- it's more how current transformation system works. Making it handling such situation correct would leat to too much overhead with space transformations and so.
It's a well-known issue and good thing to be improved, but not a bug. Closing.