The footer of pages is blank before hand, but after converting to PDF/A text and squares show up on the bottom, in the footer.
What is happening is that there are annotations at the bottom of these pages that have the Hidden and Print flags on. Meaning they are only visible when printing.
However, PDF/A requires that all annotations, including Widgets, but excluding Link type, and annotations with zero area, must have an appearance. Furthermore, the Hidden flag must not be set. In other words, PDF/A does not allow for hidden annotations.
If you truly don’t want those to appear, you would need to modify the PDF, either deleting those annotations, or setting their area to zero.