I'm playing Caster of Magic for Windows and just researched the Spell of Mastery. In the text of the spell, it says that, once researched, your spells (including SoM) cannot be "countered." As an experiment, I cast a Chaos Rift on a city protected by a Chaos Ward. I received the message, "Your Chaos Rift was countered by Chaos Ward."

So, is this a bug, or does the wording need to be tightened up?

Sounds like an oversight one way or the other. Having researched the SoM originally only made combat spells uncounterable. We had a long-winded discussion about the mechanic of Spell Blasting the SoM a few months ago though, (link), which resulted in a poll, then a subsequent change in mechanics in 1.1.0 ("-Knowing Spell of Mastery now makes all of the wizard's spells uncounterable, including overland spells and Spell of Mastery itself.").