Adding an override directory root/application/themes/elemental causes css issues

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Adding that directory to my concrete install causes it to look for the css file bootstrap-modified.css in root/application/themes/elemental/css/ instead of continuing to use the file root/concrete/themes/elemental/css/bootstrap-modified.css

Is this a bug? Is the best way to resolve this to copy the entire css directory, even if I'm only planning to add a single template?

Thanks