See Root/Pages/Kids//Annots//AP/N/Resources/Font in the attached file, it has Helv and F2. The file was produced with the CreateSimpleForm example, reloaded and modified and saved.
The cause is that when the content stream is created, the "Helv" font is added to the resources. In a classic "create a PDF" scenario, PDFBox would notice that the font is already there, but this fails, because the dictionary contains the font, so it doesn't get found (see COSDictionary.containsValue().
Solution: check the resource dictionary the hard way in PDResources. I'll do it only for fonts for now.