After Runt's encounter with the wolf ghost, Stinky makes the comment that he's "as pale as a coyote". However, Runt's coloring is exactly the same as it is throughout the entire movie.
The ghost wolf haunts Shadow Forest from Daria's childhood to when she's a young adult. Tony is portrayed as being a pup himself when he first encounters the wolf ghost, but as old as he is in the rest of the franchise, the only opportunity he could have had to see the ghost would be when he's an adult.
Daria is chased from Shadow Forest to Rabbit Poo Mountain to Shadow Forest again in what appears to be a few seconds, when it originally took them a day or two to reach Rabbit Poo Mountain from Shadow Forest when their journey began.
Shadow Forest is described as being "teeming with life", but the only animals we see in the forest are a squirrel, three porcupines, and another wolf.
Marcel claims he's trying to catch a field mouse, but mice are not part of a goose diet, it consists of small insects, fish, and vegetation. Owls normally hunt on mice not geese.
Kate reminisces to Humphrey about how their pups are growing up so fast, but they haven't aged whatsoever over the course of three movies.
The pups from both the alpha school and omega school are more or less the same age, but Tony looks significantly older than his fellow alphas.
When the wolves are exploring Shadow Forest and come to Saw Tooth Cave, Runt says "It looks like someone's home", but his mouth barely moves.
The name 'Sawtooth Cave' is used in this movie only because Sawtooth National Park was referenced in the first movie.
Rabbit Poo Mountain doesn't exist. It was only a joke that Lily made up in the first Alpha & Omega.
The ghost wolf kills/teleports that Mr. King wolf at the end, but there's no explanation of why it never tried to do that with anyone else it encountered.
Lily is a paranormal investigator and a weather girl when nothing in the previous movies indicates that she would be interested in visiting haunted forests, or that she would know anything about how to interpret the weather.