Plot hole: There is absolutely no point in getting James involved with Layla for Burke. She could have given him the program, why get someone to sabotage his own plan?
Plot hole: Wouldn't the scanner that she puts the coffee mug through be able to detect the USB connector in the bottom?
Plot hole: Why would the CIA ask Layla to test its security by stealing a real and harmful computer virus (the real Ice 9)? Unless Burke had somehow fooled the CIA into thinking what Layla was stealing wasn't real, but in that case she could have had Layla given him ice9 himself.