That certainly sounds scary, but it's not something I've experienced myself (I use that feature quite frequently) or heard about from others, and the Delete Metadata feature uses the exact same mechanisms for metadata selection as Deploy Metadata and Retrieve Metadata, so it seems like any issue there would affect those actions as well.
If you can reproduce this, please do so with
debug logging enabled for Metadata Removal and for Salesforce DX, then send me the resulting idea.log for review.
Regards,
Scott Wells