As reported by Thomas Möller on the users mailing list:
I try to overlay one pdf with another with pdfbox-app-2.0.16.
In the output pdf the overlay is rotated by 90 degrees although both input pdfs are displayed in correct orientation in Acrobat Reader.
When using PDFDebugger on the overlay pdf it shows rotate: 90
So it seems that it was rotated before and the rotation is ignored by OverlayPDF.
How it should look: