In the scene in the house, when a single alien was approaching, the dog went after him barking. Then we heard a whine, thinking the alien killed him. But later in the movie, the dog was very much alive. What exactly happened? Did the alien let him live? Was that another dog?
The dog was indeed alive in the later scenes (as the novelisation below shows).
Although it's pure speculation, I think we can be reasonably certain that the alien gave the dog a swift kick and the dog ran off scared.
Emmett ran forward to meet Jake and the riders, seeing only the black dog keeping pace with them— the friend he'd thought he'd lost forever, like so much else in his life.
The dog ran ahead down the slope to greet him, nearly knocking him over as he kneeled down to hug it, covering him with wet doggy kisses. "Hi, boy!" Emmett said, laughing for the first time that he or anyone else could remember.