I don't think it's much a problem as: Cerberus comissioned to build the original Normandy to observe Turian construction methods (I suspect the Turian equivalent was also involved) and the best donors are in the Alliance Military Industrial Complex plus Anderson and Hackett were running a Cerberys like round of experiments on the colony James Vega fought off the Collectors thanks to a developed antidote against the seeker swarms (explains why the Virmire Survivor managed to escape the Collectors on Horizon) but if you want the full actual story, see the Mass Effect movie Paragon Lost which also shows a Cerberus operative partly working with the Collectors (James Vega only says a few bits of information regarding his mission).
Yeah, that was his first time with the character and he was also working on ME3 at once.
