If you import an architectural drawing PDF into Goodnotes, you might see frames/boxes around the text in it. The same PDF shows no such frames when viewed outside the app.
It's a known issue that seems to happen to this specific type of PDFs, likely created in AutoCAD. The frames are comments that currently can't be rendered in Goodnotes.
Until there's a fix, a simple workaround is to open the file in Mac Preview and choose File > Export... and export it as a PDF. The result PDF won't have this issue in Goodnotes. Alternatively, you can open the original PDF in Chrome, choose Print, select Save as PDF from the Destination field and choose Save: