On Krita 4.0.0 Pre-Alpha and Windows 10 x64, it appears that if you enable snap to grid, and create a vector layer, and then create a square, you'll note that the created vector square shifts the point to 1 pixel right, and down.
Oh yeah, forgot to mention that the grid spacing must be 1 px, 1 px subdivision, and in rectangle form. Basically, a pixel grid.
Been fixed with the latest Krita Pre-Alpha 2. I tested it, and it no longer has this bug. Can be closed.