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.
Suggested correction: A good number of mice and keyboards connect to the computers through the USB ports. If they took out all but two ports, and left those for the mouse and keyboard, it could be possible. If Leila pulled out the keyboard plug she could put in the USB device and copy the files. Heck, she could have even opened the computer up herself and installed a hidden USB drive (smuggling in the tools with her coffee mug of course). She would just have to be sneaky about it, and that's nothing unusual for these characters.
Not only is the original "Corrected entry" valid, it's understated. Burke actually said "Langley's computers don't have disk drives" - not just no floppy drive. In a high-security environment, such a system would be configured so that no USB port could communicate with an external drive; even more likely, the workstations would be dumb terminals - just keyboard, mouse, and monitor; and that's exactly what they appear to be in Layla's office area. So, showing a USB port built into Layla's keyboard and communicating with a USB drive belies a major part of Burke's story, and if Layla were able to do that, the system would immediately "see" it. It's the ersatz "Correction" that's mistaken, since it describes only ordinary commercial computer systems.