The website that hosts uTorrent was hacked by an unknown person or group.
After initially stating that the "mainline" BitTorrent site had been hacked as well, the company now says that it doesn't think that BitTorrent.com was affected.
According CNET, the proper executable files for both programs were replaced with "a fake antivirus 'scareware' program" called Security Shield. The company shut off the download spigot at around 6 a.m. and has since restored the proper download files. BitTorrent advises that anybody who downloaded the programs between 4:20 a.m. and 6:10 a.m. PT runs a security scan.
Removing fake antivirus programs, which are almost always a kind of rootkit, can be notoriously tricky. It's advisable to start with Anti-Malware to determine if there actually is an infection.