The scene with Tim having made a specialised thievery app is basically him peacocking and Tony being "OMG. MY BOYFRIEND IS SO SMART." Tim knew Tony was going to try and grab the phone, he just wanted a little public contact and to tell his conscience he was coerced, but really, it was all complicit. (Tony's expression and tone as he acted as Tim's desk? Oh wow.)
The scene with Ducky and Gibbs at the end? Gibbs' smile? I know they were talking about Sophie, but it seriously looked like Gibbs was about to kiss Ducky. Hee!