It was a movie starring a living rubber duck along with other rubber toys. The first thing i recall about this movie was a scene where, on a cargo ship carrying crates filled with toys, the rubber duck asked a bunch of black, cycloptic hexagonal toys to let him join in their crate but one of those hexagons rejects him as its eye turns into a 🚫. The second thing i recall is that near the end of the movie, the rubber duck's friends squish him, as if they were trying to hug, and the duck does the quack sound rubberduck toys are known for and they get confused about where the sound came from, not knowing it was the duck who caused it (throughout the movie, the rubberduck wasn't able to quack, because of some design fail). I recall this movie appearing in Disney Jr.
You should look up Lucky Duck, from what i found it's a Disney Jr. movie about a duck getting thrown off a cargo ship and that sounds just like the movie you described.