The error appears to indicate (though not very clearly) that the document does not have physical units set. Files that you plot are required to have physical units (typically inches or mm), and trying to plot files constructed for screen display can sometimes give unpredictable results.
I am not certain that this issue is (or is not) directly related to the layers issue.
As a first suggestion, please try plotting one or more layers from the “birthdayCard_outlines.svg” example file, just without pen or paper. You can find that file in our standard example set download, in the “from launch video” folder.
If that file plots correctly, it would suggest that there is an issue specific to something in your file. If it does not, then there’s likely something amiss in your software setup. In either case, it should point the way forwards.