I received the Berserker expansion, Wraiths expansion and Rune Golem expansion for Xmas, and noticed that the upgrade cards included with the 'Zerkers and Wraiths are the same size as the unit cards. Is this an error or the way going forward, like X-Wing 2.0 went?

It's the way it's going forward. Old cards are still organized-play-legal, but if anything gets reprinted, expect it to have the larger cards and (presuming any terrain fits) the smaller boxes.

Xelto, when did FFG (if they did) announce they were doing this? Just caught me unawares.

It just kind of happened. I think it was when they delayed everything for 6 months and the packaging changed to smaller boxes.

So everything after the uthuk core release has big cards.

A lot of the cards also got more wordy around that time.