In a February 2008 interview with thewho.com,band frontman guitarist Pete Townsend admitted the album "is no longer a complete set of masters. An entire side has been stolen from our vaults at some point." Since the master for Won't Get Fooled Again is already in the core game, the missing half is probably side 1 of the album, which includes classics like Baba O'Riley and Bargain. "These things happen," Townsend said by way of explanation.
Of course, there's nothing to say these tracks couldn't be replaced with cover versions in an eventual download pack, but this would seem to go against the spirit of the full album download program, at the very least. We've asked Harmonix for a comment on this story and will let you know if and when they respond.