In this revision of Columbia University tunnels on enwiki, reference 1 is used in two places. The first use is inside a {{Quote box}} template. I deleted the template in this edit, which also deleted the reference, resulting in this revision which gives "Cite error: The named reference auto was invoked but never defined"

Normally, if you delete the first copy of a multiple-use reference, VE will transfer the citation to another instance which still exists, like it did here. Having the reference inside of a template seems to prevent that from happening.