When Shadow falls into a pit and injures his leg, the dog never actually fell into the pit. When he stepped on the boards, they broke, but there was a platform immediately below. Then a fake dog was dropped into the pit and these scenes were edited together. Shadow tries to get out but the pit is large and deep and muddy and he keeps slipping back into the pit because he cannot get a good grip. To accomplish this scene, a special pit was dug which was about three to four feet deep. For the sliding back and forth, one trainer was at the top of the pit calling the dog. Another trainer was at the bottom telling the dog to stay. When he did, he would naturally start sliding downward. The dog could actually walk out on his own at any time and did so several times during the filming. When Shadow does appear at the end of the film to be reunited with Peter, Shadow runs with a limp. This was accomplished by putting part of a round wooden bead between the dog's toes. The bead did not hurt him in any way, but gave him a peculiar sensation, causing him to walk with a limp.

The marks on Chance's face from getting hit by the porcupine change in nearly every shot, and at one point disappear all together, but are back in the next shot.

Some additional scenes not included on the video release but aired on TV include:

• A scene where Peter and Jamie wash off Chance after he eats the wedding cake but before he tricks Sassy on the seesaw.
• A scene in which Kate takes the animals for a ride in the truck.
• A scene with the kids playing Nintendo when Bob realizes he's been invited to a welcome BBQ on the same day they were supposed to go to Kate's to visit Shadow, Chance, and Sassy.
• An extended scene of Quentin rescuing Sassy and taking her back to his cabin.
• The scene where Frank greets Kate upon her return home was extended to show Kate discovering the missing part of her note, calling an animal shelter, and speculating to Frank that the animals left to head home to Fresno before calling a park ranger.
• A scene where Quentin is playing the saxophone during the evening and then Sassy tying up Quentin's goat when he left his cabin.
• After seeing the Fresno skyline and before hitting a rail yard, the animals stop at a dumpster where Sassy tries to find food but comes up empty.

Featured in Siskel & Ebert: National Lampoon's Loaded Weapon 1/The Cemetery Club/Sommersby/The Vanishing/Homeward Bound: The Incredible Journey (1993)