User blog comment:Legionwrex/How did Saren reach the Citadel?/@comment-2250460-20130507164142/@comment-1440333-20130507181401

Ok here's another suggestion, he came through in a vehicle, it didn't crash and is off somewhere else on the Presidium wreaking havoc. Or alternately his ship did crash, and the Keepers cleared the wreckage away before Shep arrives - after all we know how fast they can work.

Its most likely that Saren was already at the end of a significantly large column of troops and vehicles, as this is the only way to explain exactly how many troops are on the Citadel, as well as how much damage the Presidium has already sustained.