Generally speaking, a farm requires farmers. If you have a large population of clones or whatever that you're looking over until they become useful, you need staff: people to maintain order, people to teach them (if you decide they need to know anything), people to make sure they eat right and exercise (if you need them in a certain physical condition), people to make sure no one gets out, people to make sure no one gets in... staff. Staff need managers. Managers need meetings, agendas, reports. Outside investors need to be apprised, or at least reassured that things are going smoothly. Whoever you're farming people for needs to take possession of them.
The logistics and general backend of an operation like this would be considerable, and chances are that it leaves a hefty paper trail. If anyone stumbles across that paper trail, they could blow the whole operation wide open. Even if they don't, observing the staff could easily tell them that something isn't right, even if it's not immediately obvious what that is.
For instance, if the farmees generally believe that they get picked at intervals to be reintegrated into normal life, and they discover that there are big meat lockers on the island with no particular purpose, and people are seen wheeling freezers in and out of there around the time of each shipment to the mainland, well, they might get a little suspicious.