Thanks for the report.
Looking at the code, they shouldn't be there.
The redirect_virtual_host.conf template does use tokens, but doesn't accept any custom conf files or things like that.
The list is from the /etc/virtual/domainowners file, so I've added one extra check during popluation to see if the data/users/username/domains/domain.com.conf file exists, and if it doesn't, it's remove from the list.