If you ever need it, WebUI compiler has flags to disable some features. For example, you can use --no-css to disable processing of css. You can either pass these flags when invoking dwc from the command line, or if you are using build.dart, you need something like this:
var args = new Options().arguments.toList();
args.addAll(['--', '--no-css']);
build(args, ['your_entrypoint.html'])
WebUI tries to process any css file that can be reached via relative paths from the entrypoint file. If you provide absolute paths or http URLs for css classes, WebUI will not process those links either. That would let you remove the warnings, while still processing CSS everywhere else.
If you have a local dev server, you can use a project-absolute path (instead of a file-system absolute path) to get things working.
If you can, please do open a bug with more details to track the source of the problems you saw.