User blog comment:Tiredman2/Mass Effect Plot Holes and Contradictions/@comment-24.76.84.236-20120824032415/@comment-5337704-20120824152821

According to the Mass Effect Timeline...

The events of Mass Effect 2 begin. One month after the Battle of the Citadel, the SSV Normandy is attacked and destroyed by an unidentified assailant, resulting in the death of Commander Shepard. Later, the Systems Alliance officially declares Shepard "killed in action".

Of course anything can be left to the imagination as: Shepard had the new prototype, or possibly some how new about the upcoming changes to the weaponry. Sadly, I dont think there is really a way to explain this one.