When Jesse first feeds Willy, he throws a headless fish into his tank. When Willy brings it back to him, it has a head.
When Randolph asked Jesse if he had ever looked into Willy's eyes, he said, about orcas, "Those eyes discovered the stars long before man was even a whisper on this Earth", but later when telling Jesse the Haida story about Natselane, he said "Natselane was a Haida who lived long before there were orca whales".
When Willy and Jesse are pulled out of the tank, both are soaked. But as they put Willy onto the trailer, he is still wet, but Jesse is completely dry.
When Willy is being brought out of the tank the water level is shown at 8 ft. But in the next shot you see Jessie and Rae getting Willy in the net, the water level is marked off at 11 ft.
Since all the scenes in the movie were shot out of order, Jesse's hair can be seen in a mullet or with long hair in scenes shot in Mexico. But for the scenes shot in Oregon, he has short hair.
Michael Madsen, August Schellenberg and Lori Petty's doubles are seen briefly when Glen backs the truck containing Willy into the water.
The Indian Folk Tales book Randolph reads to Jesse misspelt Nastelane's name as Natsilane.
When Willy is jumping over the stone wall at the end of the movie, the bottom of the actual whale does not match the pattern of the CGI whale that lands the jump.
(at around 1h 18 mins) When Randolph and Jesse are looking at the leaking tank for the first time, Randolph says "It's part of the tank", his lips do not move.
When Jesse and the other street kids find out they haven't gathered enough money to buy food, Perry says "Shoot, I'm hungry!" But his lips mouth "shit" instead of "shoot".
When Randolph is using the crane to lift Willy out of the tank you can see the reflection of a man in the crane window.
The highway with the tunnel entrance is actually located in Chinook, Washington in real-life which is nearly 40 miles away from the marina in Warrenton, Oregon.
When Rae and Jesse were in sorting fish to give to Willy, Rae says that they give Willy the good fish and not the "bad fish" (fish that were cut up and had no head). However, Jesse is seen putting some "bad fish" in the good fish pile.