Steps to reproduce:

• open page in VE
• insert a reference
• select the reference and use copy/paste to duplicate it (you'll end up with something like <ref name=":0">blah blah</ref><ref name=":0" />)
• open the second instance of the reference and edit it

This is a very natural workflow: I write stuff, then copy and modify it to obtain a slightly modified second instance (references to different pages of the same book and so on). What actually happens is that the second reference remains a duplicate, and the first reference is changed (and the old reference content is lost). This is very unintuitive, and can result in errors without the user even noticing. There is a warning about editing a reference that appears in multiple places, but it's easy to miss and it's not very clear what it warns you about.

I think the least problematic approach would be a Google Calendar style "[ Edit this instance ] [ Edit all instances ]" dialog.