In Onionizing Repositories#Debian_Templates users are instructed to add debian.list to Qubes Debian templates. When following these instructions and running apt-get update I get this output.
W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:5 and /etc/apt/sources.list.d/debian.list:5
This happens on Debian templates that are up to date but not on Debian templates that have never been updated.
I also have Qubes repos onionized but I don’t think that is the issue.