Note that some changes were made to production last sync... the droids will appear in the inventory of the owner of the factory now. I'm not sure if that is the reason for this specific situation, but if your factories are owned by someone else and are being rented by you, that may explain the whereabouts of the droids. This change is slated to be changed
because it is causing logistical issues for many small producers.
If that is not the situation and the factories are owned by the entity whose inventory you were checking for them, that does sound like a bug.