Factual error: Hooch is a french mastiff. The dog he gets pregnant is a collie. Different breed dogs do not make purebred puppies. Hooch's pups would be part collie, part mastiff. In the end of the movie, one pup is pure mastiff like hooch and 4 are pure collies like their mother.
Continuity mistake: While Tom Hanks is driving to the motel after leaving the fish packing plant, scratches are on his face and blood is on his ear. When he pulls into the parking lot of the motel, the scratches are gone.
Continuity mistake: When Turner is taking Hooch to see the vet and he is running alongside the car, on the long pole with his leash dangling behind him. In some shots the leash is secured to his collar and in others it is just loose.
Plot hole: David Sutton claims he's never read an autopsy report before yet earlier he said he moved to his new town to get away from all the murders he investigated, a job that would have required him to read autopsy reports.
Continuity mistake: Turner goes to see the old man and brings Hooch a muffin as a gift. Hooch knocks Turner down and the muffin goes flying and lands upright. When Hooch goes to get the muffin, it is laying on its side.
Factual error: When the police search of the fish packing plant, a policeman stirs through the lobster tank with a pole looking for evidence. The mistake is the lobsters are all red - live lobsters are deep brownish green - cooked lobsters were put in a lobster tank for the shot. There is no reason to keep cooked lobsters in a tank of water at a fish packing plant.
Continuity mistake: When Turner is on stakeout with Hooch, Turner is wearing glasses when he tastes the dog biscuit. When he feeds the biscuit to Hooch you can see his glasses on the dash. He then puts them on again in the next shot.
Audio problem: When Turner is playing with Hooch in his living room, Hooch is chasing Turner and barking at him. However, the audio of the barking is way out of sync with any movements of Hooch's mouth.
Continuity mistake: When Hooch is pulling against the leash and yanking the desk towards the stairs, the leash is connected to the non-choke chain on his collar. In all previous shots it was in the choke chain of his collar.