I recently took my trilogy wide. I signed up for Smashwords, ONLY so I could distribute through Smashwords. Another site to reach readers, right?
I logged in to my account yesterday only to discover they'd added my book to a "premium" catalog and had started distributing it to Amazon, Barnes & Noble, Apple, etc. I had registered sales there. But I am direct to those sites, ergo don't want Smashwords distributing there and taking a cut. I am fairly certain I opted to only put my books up via Smashwords, but for some reason, I don't know if it's automatic with premium catalog or there was an error, they were distributing to sites to which I am already direct.
Long story short. Go back and double check your settings!