I've noticed that this seems to happen when you are adding units to the production queue in "all production" mode (as opposed to production for a specific hex) and a new production center has come on line while there are queued units. It seems like none of the units are assigned to the new production center until the queue is empty. I get around this by specifically selecting the new production center and queuing up units for it.
This is true. Aready queued units will not "shift" to newley finished factory. Cancel them and start building them again at the new location.