So you build Alliance cruisers with an Alliance company then somehow steal them from Alliance docks then stash them somewhere? Bioware writers logic is beyond understanding.
It's just something I kicked around in the back of my head. 
Bare in mind, Cerberus did start off life as a black ops group for the Alliance, at least on the surface. They probably know of secret bases that the rest of the Alliance wouldn't have been privy to. I also wouldn't be surprised if the Alliance accepted some privatized funding, which I think would be one Mr. Harper. When the black ops group went rogue, they took their classified information with them, which included any bases, hangars and/or otherwise secret locations. That would include any cruisers or other parts of a larger fleet that they might have either been working on, or given by the Alliance. They also probably went out and bought some of their own ships. Maybe not the larger ones, but certainly some of the smaller craft that they have.
Alliance brass probably didn't want to know everything that their black ops team was up to, for the sake of plausible deniability. The Traverse is a big place, and very hostile to the Council (and the Alliance, naturally.) Make the right arrangements with the right colonies, governments, and black market dealers, grease the right palms and yeah, I could see it for sure. Again, Alliance brass was very unlikely to know or even want to know what kinds of arrangements had been made. By the time that Cerberus played their full hand, the Reapers were already there and everyone was too focused on that to look into where all the Cerberus ships came from. That's how it's done, in my opinion.
Guys, can we please leave real world politics and terrorist organizations out of this? The posts tend to get nuked and can lead to a thread lock.