Program: 150666
Project: 150666
Buggy source:
@Override protected void paintInPanel(AffineTransform tran,Graphics2D g2){
  DetectQrCodeControlPanel controls=(DetectQrCodeControlPanel)DetectQrCodeApp.this.controls;
  g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,RenderingHints.VALUE_STROKE_PURE);
  g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
synchronized (DetectQrCodeApp.this) {
    if (controls.bShowContour) {
      List<Contour> contours=detector.getSquareDetector().getAllContours();
      g2.setStroke(new BasicStroke(1));
      VisualizeBinaryData.render(contours,null,Color.CYAN,scale,g2);
    }
    if (true) {
      FastQueue<QrCode> detected=detector.getDetections();
      g2.setColor(new Color(0x90FF0000,true));
      for (int i=0; i < detected.size; i++) {
        QrCode qr=detected.get(i);
        VisualizeShapes.fillPolygon(qr.bounds,scale,g2);
      }
    }
    if (controls.bShowSquares) {
      List<Polygon2D_F64> polygons=detector.getSquareDetector().getPolygons(null);
      g2.setColor(Color.GREEN);
      g2.setStroke(new BasicStroke(3));
      for (      Polygon2D_F64 p : polygons) {
        VisualizeShapes.drawPolygon(p,true,scale,g2);
      }
    }
    if (controls.bShowPositionPattern) {
      FastQueue<PositionPatternNode> nodes=detector.getDetectPositionPatterns().getPositionPatterns();
      g2.setColor(Color.ORANGE);
      g2.setStroke(new BasicStroke(3));
      List<SquareEdge> list=new ArrayList<>();
      for (int i=0; i < nodes.size(); i++) {
        SquareNode n=nodes.get(i);
        VisualizeShapes.drawPolygon(n.square,true,scale,g2);
        for (int j=0; j < 4; j++) {
          if (n.edges[j] != null) {
            if (!list.contains(n.edges[j])) {
              list.add(n.edges[j]);
            }
          }
        }
      }
      g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,RenderingHints.VALUE_STROKE_PURE);
      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
      g2.setColor(new Color(255,150,100));
      g2.setStroke(new BasicStroke(3));
      Line2D.Double l=new Line2D.Double();
      for (int i=0; i < list.size(); i++) {
        SquareEdge e=list.get(i);
        Point2D_F64 a=e.a.center;
        Point2D_F64 b=e.b.center;
        l.setLine(scale * a.x,scale * a.y,scale * b.x,scale * b.y);
        g2.draw(l);
      }
    }
  }
}

Fixed version (ground truth):
@Override protected void paintInPanel(AffineTransform tran,Graphics2D g2){
  DetectQrCodeControlPanel controls=(DetectQrCodeControlPanel)DetectQrCodeApp.this.controls;
  g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,RenderingHints.VALUE_STROKE_PURE);
  g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
synchronized (DetectQrCodeApp.this) {
    if (controls.bShowContour) {
      List<Contour> contours=detector.getSquareDetector().getAllContours();
      g2.setStroke(new BasicStroke(1));
      VisualizeBinaryData.render(contours,null,Color.CYAN,scale,g2);
    }
    if (true) {
      FastQueue<QrCode> detected=detector.getDetections();
      g2.setColor(new Color(0x50FF0000,true));
      for (int i=0; i < detected.size; i++) {
        QrCode qr=detected.get(i);
        VisualizeShapes.fillPolygon(qr.bounds,scale,g2);
      }
    }
    if (controls.bShowSquares) {
      List<Polygon2D_F64> polygons=detector.getSquareDetector().getPolygons(null);
      g2.setColor(Color.GREEN);
      g2.setStroke(new BasicStroke(3));
      for (      Polygon2D_F64 p : polygons) {
        VisualizeShapes.drawPolygon(p,true,scale,g2);
      }
    }
    if (controls.bShowAlignmentPattern) {
      List<QrCode> codes=detector.getDetections().toList();
      g2.setColor(Color.BLUE);
      g2.setStroke(new BasicStroke(3));
      for (      QrCode qr : codes) {
        double size=Math.sqrt(qr.ppCorner.areaSimple()) / 14.0;
        for (int i=0; i < qr.alignment.size; i++) {
          QrCode.Alignment a=qr.alignment.get(i);
          VisualizeFeatures.drawCircle(g2,a.pixel.x * scale,a.pixel.y * scale,size * scale);
        }
      }
    }
    if (controls.bShowPositionPattern) {
      FastQueue<PositionPatternNode> nodes=detector.getDetectPositionPatterns().getPositionPatterns();
      g2.setColor(Color.ORANGE);
      g2.setStroke(new BasicStroke(3));
      List<SquareEdge> list=new ArrayList<>();
      for (int i=0; i < nodes.size(); i++) {
        SquareNode n=nodes.get(i);
        VisualizeShapes.drawPolygon(n.square,true,scale,g2);
        for (int j=0; j < 4; j++) {
          if (n.edges[j] != null) {
            if (!list.contains(n.edges[j])) {
              list.add(n.edges[j]);
            }
          }
        }
      }
      g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,RenderingHints.VALUE_STROKE_PURE);
      g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
      g2.setColor(new Color(255,150,100));
      g2.setStroke(new BasicStroke(3));
      Line2D.Double l=new Line2D.Double();
      for (int i=0; i < list.size(); i++) {
        SquareEdge e=list.get(i);
        Point2D_F64 a=e.a.center;
        Point2D_F64 b=e.b.center;
        l.setLine(scale * a.x,scale * a.y,scale * b.x,scale * b.y);
        g2.draw(l);
      }
    }
  }
}