Create a scratch org, try and sfdx force:source:deploy -m LightningComponentBundle
or sfdx force:source:deploy -u 1099-repro -c -m AuraDefinitionBundle
and it should fail (without a useful warning). Go into the Org and inspect the deployment to see the failure. An object 'withoutContent' of type LightningComponentBundle was named in package.xml, but was not found in zipped directory