I do remember reading an article that when they were converting some films to 3D (Finding Nemo was mentioned), they had to adjust the layout of objects in a scene, and in the case of Nemo, reduce the amount of bubbles and stuff suspended in the water because in 3D it was too distracting.
Yeah, to clear up confusion, changes like that are what I was referring to as “fixes” earlier.
Someone in this thread supposedly worked on the re-renders for TS1 and 2, who goes into the process better than I can. I’m not sure if the exact same stuff was done for the Nemo, Monsters, Inc or other Disney re-releases but it’d make sense if so.