After all open spaces on each FOB deck are full, newly recruited soldiers begin automatically going into the waiting room. Once the total number of soldiers on the FOB (including those in the waiting room) exceeds a maximum value (I think it's around 700), then any time new soldiers are extracted or the FOB receives volunteers, you get a message saying that soldiers were dismissed due to overcrowding.
How does the game decide who to dismiss? Are the soldiers just turned away when the FOB is full, does it try to choose the soldiers with the lowest stats, or is it just random? Having to go through the waiting room and find my least qualified soldiers one by one and dismissing them is tedious, but I'd rather do that than risk having the game dismiss a highly rated soldier I just fultoned in because I don't know how the system works!