Back in 2008, a couple's dog was shot and killed during the execution of a no-knock warrant performed by the paramilitary SWAT. They are now suing Howard County over the raid. The two were acquitted of any charges and it was an acquaintance at the resident in possession of drugs, not the couple themselves (who have no prior criminal record).
I'm not necessarily buying all the claims made in the lawsuit, but SWAT has been known to shoot dogs through screen doors and, in another Maryland case, shot and killed dogs running away from them so I don't find it surprising they might take out the dog(s) first.
The article also refers to the February 2009 incident in which Howard County SWAT invaded a home and killed the family's dog. In the article above, officials claim Howard County SWAT had a really good reason to invade the home - stolen weapons. That were never found, by the way, and that had nothing to do with the family actually in residence at the time (the step-son was the guilty party and hadn't lived there for three years).