This first scene that was cut was apparently some kind of scene introducing us to the characters of Kate and Dan. This explains why they both float towards the camera in the final film when we first see them.
The second scene cut is when the survivors of the Palamino are escaping the doomed Cygnus and run through some kind of engineering catwalk. Charlie almost falls into some smoke and V.I.N.CENT rescues him. This scene is still present in Alan Dean Foster's novelization. I'd love to believe that they shot the well known alternate ending, where Kate is in the Sistine Chapel looking at the Creation of Man, I think that ending would have brought something more to the film in terms of scope. As much as I would love to peruse the Disney vaults, I think that we may have to wait and see if any Blu-ray release will include these scenes.