Maya 2016's target weld behaves differently from previous Maya versions. When you select verts in vertex mode it remembers the selection. Now when you use the target weld tool, it automatically goes back to selecting the vertices that were previously selected in vertex mode. This is a problem because sometimes you switch…
Multi-cut does the same thing, and I keep running into it remembering the "wrong" selection, or one from several selections ago. I'm not sure about the target weld tool, but you can't deselect in the void with multi-cut. You may want to edit your hotkey or marking menu to go to vert mode, deselect all, then enter the tool?