Board Thread:WARNING ALL USERS False Info\Spoilers/@comment-166.137.156.44-20140108021332/@comment-108.201.175.15-20140109002327

The show may of not used a real coyote, but the synopsis for the next episode (More Bad Than Good) clearly states that it was indeed a WereCoyote:

"Scott and Stiles continue to search for the Werecoyote. ..."

You can find several recaps for the episode that say Scott was chasing a coyote. As far as we are concerned, it was a coyote... whether they used a real one or not.