Ass Pull: The American dub team clearly decided Milo and Otis needed to return to the farm to have a happy ending, yet there was no footage in the original version to suggest it. So they simply randomly decide a road they've found will take them back there.
Audience-Alienating Premise: Thanks to the allegations of animal abuse, people are scared off from watching the movie. Even when the allegations are unproven and no foul play was involved, people are uncomfortable at certain scenes where the animals must have been put in stressful situations.
The original Japanese version has the recurring melody "Watage no Hara", a beautiful and nostalgic-sounding piano piece by Ryuichi Sakamoto.
And, of course, the English dub has that Dan Crow's charming and nostalgia-inducing "Walk Outside".
Harsher in Hindsight: For people growing up loving the film, only to later learn of the animal abuse allegations surrounding its production. Even when not counting the allegations, some of the scenes, such as the infamous cliff scene, can be hard to watch as an adult.
Narm: For people used to the Japanese version, or even certain non-English dubs that kept the dark narrative of the former, the Lighter and Softer-turned English version can come off as this.
Overshadowed by Controversy: The allegations of animal abuse behind the scenes are talked about more often than what actually happens in the film.
Squick: When we see close-ups of the mates of both Joyce and Sondra giving birth. It doesn't help if you know that Pugs, having been specifically bred for cuteness and nothing else, have a very difficult time giving birth without surgical assistance. Dudley Moore, as he voices all the characters, spending a very solid amount of time on Joyce's breathing during labor.
The Woobie: Both of the title characters simultaneously; Milo - who is hurt by a crab as a kitten, and crying for help (on deaf ears) as he floats on a rushing stream of waterfalls, gets mobbed by a horde of angry seagulls, and falls into a hole- that is until his best friend Otis rescues him. And Otis- who tries to save his best friend Milo, only to be separated from him, and is pinched by a lobster, almost drowns in the sea, and nearly dies of hypothermia when trying to find food for his offspring in the winter!Hearing their cries for help will break your heart!
, a beautiful and nostalgic-sounding piano piece by Ryuichi Sakamoto.