According to the NYT, the revelation was due to the emails being forwarded from Broadwell. So as almost always is the case in real life, it seems the security breach was through a social lapse, not through a technical obstacle. And it was not movie-like/CSI-level sleuthing, but just an accident, that the authorities found out
> WASHINGTON — The F.B.I. investigation that led to the resignation of David H. Petraeus as C.I.A. director on Friday began with a complaint several months ago about “harassing” e-mails sent by Paula Broadwell, Mr. Petraeus’s biographer, to an unidentified third person, a government official briefed on the case said Saturday.
http://nyti.ms/RLx6QT
> WASHINGTON — The F.B.I. investigation that led to the resignation of David H. Petraeus as C.I.A. director on Friday began with a complaint several months ago about “harassing” e-mails sent by Paula Broadwell, Mr. Petraeus’s biographer, to an unidentified third person, a government official briefed on the case said Saturday.