To expand upon Michael's post:
Missions are a subset of Shadowrun adventures, and will generally either part of the "seasons" of the Living Campaign, or Convention Mission Packs (CMPs) which take place during a given season, but don't generally directly relate to the story arcs of the main season. They're identified by having "Shadowrun Missions" in the name and by the Shadowrun Missions logo.
What's in Coyotes is an adventure, just like Splintered State (though clearly smaller in scope).
So: all Missions are adventures, but not all adventures are Missions. Confusion sets in because people sometimes use the words interchangeably.