This might be a long shot with how little I remember of the movie. I only remember one scene, where a small dog flies through a window knocking a man out. Then it shows the man laying there while the camera pans away to show a dog staring at him menacingly. The movie either had to do with a spirit, parasite, or alien that could take over animals' bodies
Possibly Suspiria directed by the great Dario Argento, containing this scene with a seeing-eye dog attacking and killing its master. Suspiria is about a dance school which is a front of a coven of witches.
Warning: this is a horror movie and the video below is meant to be scary and possibly NSFW as a result.
"The title character is a murderous white Bull Terrier who tells the story of his search for a proper master in voice-over narration."
Could it be "Vampire Dog"? It has a small dog. The dog moves fast enough to appear to be flying. He knocks a guy over into a vat of jello. It's eyes are creepy.
This is a long shot, but maybe you're thinking of Night of the Creeps (1986).
The details which fit:
- Alien parasites which can take over bodies (both human and animal)
- There's a creepy parasite-infected dog which is pivotal to the movie
The details which don't fit:
- I don't believe the dog ever flies through a window. It does cause a bus crash and it does look menacingly at a couple of people.
Wasn't a dog infected by the parasite in The Hidden (1987)? Not sure about the flying through the window part, but the rest fits.