"There has been a widget with a missing page reference" and non widget annotation gets flattened

PDDocument doc = PDDocument.load(new File("PDFBOX-4636.pdf"));
List<PDAnnotation> annotations = doc.getPage(0).getAnnotations();
PDColor red = new PDColor(new float[] { 1, 0, 0 }, PDDeviceRGB.INSTANCE);
PDColor blue = new PDColor(new float[] { 0, 0, 1 }, PDDeviceRGB.INSTANCE);
PDAnnotationCircle circleAnnotation = new PDAnnotationCircle();
circleAnnotation.setContents("Circle Annotation");
circleAnnotation.setInteriorColor(red);
circleAnnotation.setColor(blue);
circleAnnotation.setRectangle(new PDRectangle(100, 700, 100, 50));
circleAnnotation.setPage(doc.getPage(0));
circleAnnotation.constructAppearances();
annotations.add(circleAnnotation);
doc.save("PDFBOX-4636-annotated.pdf");

doc.getDocumentCatalog().getAcroForm().flatten();
doc.save("PDFBOX-4636-flattened-bad.pdf");
doc.close();

doc = PDDocument.load(new File("PDFBOX-4636-annotatedAP.pdf")); // PDFBOX-4636-annotated.pdf opened with Adobe and saved
doc.getDocumentCatalog().getAcroForm().flatten();
doc.save("PDFBOX-4636-flattened-good.pdf");
doc.close();