The application requires a small, inert molecule, which PFOA was, in spades. They simply made a slightly different small molecule that was almost as inert.
Small is a problem because it becomes mobile. Inert is a problem because it doesn't easily break down. Now, instead of having one "forever chemical" we have a host of them in the environment.
Not sure what the right answer is and whether we are actually better off as a result of all that work.