This may sound naive, but it is entirely possible that those dealing with the vaccines issue didn’t comprehend at all what political difficulty this would cause

Not everyone who works for EU worked on the protocol, or Brexit. And in a crisis, stove-piped process often takes over https://twitter.com/philip_ryan/status/1355258434552274946

To give another example, something similar-ish happened when the EU agreed a DCFTA with Ukraine in 2013, which then sparked Maidan etc.

I was in Bxl at the time, and no one foresaw Russia annexing Crimea as a result of a trade deal (that most Ukrainians wanted).

Again naive?

FWIW, Imho, today’s episode shows the real weakness of the EU system:

There is no executive to bring all these aspects together, both technically and politically.

EC mainly does technical, Council mainly does political, but separate (often competing) institutions. Then the EP.