In Graphics2D drawing a filled rectangle with a 1-pixel border shows a correctly filled rectangle, applying the same code with SVGGraphics2D results in a misalignment of the border and the filled rectangle:

SVGGraphics2D graphics = new SVGGraphics2D(40, 40);
graphics.drawRect(10, 10, 20, 10); // 1- pixel border
graphics.setColor(Color.BLUE);
graphics.fillRect(11, 11, 19, 9);

The method drawRect of Graphics2D internally draws four lines to get a rectangle, it seems in SVG the x,y starting-coordinate of lines is not the top-left corner but the middle of the lines which causes the misaligment.
Unfortunately the class SVGGraphics2D is final so no easy workaround can be implemented.