Cybersecurity

In terms of her getting the intel on Penny, it's demonstrated earlier in that episode when Ironwood displays a holograph of his airships around Beacon. As he removes his scroll from Ozpin's projector-desk, you can see the "black queen chess piece" logo that Cinder was using appear on his scroll as well, indicating a successful transfer of the virus.

I think Cinder uploaded the virus to the local Beacon Academy campus network, while Penny's info was kept on the Atlas Military's own separate, classified network. Presumably cybersecurity for the CCTS is good enough that Cinder couldn't hack the full global telecom network, so she was just getting info that Beacon Academy had publicly available on their campus wifi - until Ironwood's hubris about the strength of his conventional defenses, and his need to "show off" his strength, ended up compromising the Atlas military network as well.

/r/RWBY Thread