When you add a new citation in VE, templates which wrap the <references /> tag do not update to display it until the page is saved. Examples include [[https://en.wikipedia.org/wiki/Template:Reflist|{{reflist}}]] on the English Wikipedia and [[https://es.wikipedia.org/wiki/Plantilla:Listaref|{{listaref}}]] on the Spanish Wikipedia. This bug doesn't block any of the core citation workflows (creating, editing, and reusing) since those are accessed from the toolbar and the in-text reference numbers, but it's still very annoying.
However, it remains unfixed because it's an extraordinarily hard technical challenge, verging on impossible given the current architecture of Mediawiki. No one has any idea what a workable solution would look like. Just to give one facet of the problem, you could implement this in VE right now if you completely re-parsed the entire page every time the user touched a template or a reference—which would be a horrible user experience and place insane loads on the servers. It's possible that in the future, someone will think up a brilliant solution that avoids all these huge issues, so this task remains open.
In the meantime, the planned solution is to update the <references /> tag, which does update properly during editing, to support multiple columns and alternative list styles so they have all the functionality of these templates (T53260). When that task has been completed, communities will be able to replace the templates with references tags at whatever pace and with whatever tools they prefer (if there's demand for it, it would probably be possible to do a more immediate, bot-driven changeover).