Having been on the ride a few weeks ago, I have to admit that I didn't notice anything that jumped out at me as not functioning correctly... other than the final E.T., who did not say my name (or the names of anybody else in my group).
Other than that, I thought everything looked and sounded fine. But as someone who only gets to visit every few years, I don't have all the intricate details of the ride committed to memory, so I guess it's possible that stuff wasn't working and I just didn't notice.