When Raj and Auggie are watching the ship 'Judgement Day' from the screens in the control room, you can see that the headsets Raj and Auggie are using, are changing in between takes. The type of microphone on the headsets change.
When Wade is heard saying, "Picking you up," his mouth does not match his words.
The organization intended to cut out the entire ship and crew with nano fibers in order to get hard drives before they are destroyed by the crew during an open assault. THere is no way they could be sure that the nano fibers wouldn't slice those hard drives too.