Or maybe they did the same as McCoy did and Khan told them how to move them to the portable pods without unfreezing them. Or maybe Data's head tripped not only the guy doing the genetic engineering, but the designer of the pods. Or maybe that was decoy Khan from the decoy Botany Bay, with the real one still out there. Or maybe nuAnnorax altered Earth's past to deal with nuJaneway for good. Or maybe someone behind the scenes mixed up the pods of Khan and the people from TNG: The Neutral Zone, and Director Marcus yelled "Someone... WHO?"