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Think this is related to the change to the new renderer; manipulating a vertex by click-drag-drop moves it to an unexpected position.
Seems to occur in first-person as well as third-person view.
Imo vertex drag&drop is one of the most dangerous and error prone function of the editor. I am considering to remove it completely for a while already.
It can be, yeah - direct manipulation is one of the easier ways to get irregular areas (caves etc) to look the way you want them though. As always, there are other ways to do it, but I would miss it.
(...I suppose that would carry more weight if I were actively making levels!)
Vertex drag-drop was fixed in one of the recent versions, don't remember which right now.