I think some felt that Toy Story 3 should have ended differently because they thought it could have had more closure for certain plot points or they had hoped for a twist that didn't happen. It's all about what each person imagines as the perfect ending.
Some people might think Toy Story 3 should have ended differently because they felt certain characters' arcs weren't fully resolved or they had a different vision for the overall message of the story. Also, personal preferences play a big role. Some might have preferred a happier or more bittersweet conclusion.