Look's like that you can hire only one time 12 soldiers,
else when you hire soldiers second time, previously hired soldiers can just removed from both "personal"&"soldiers" screens but they are still present in "assignment" window of "soldiers" screen and on "aircraft" screen.
It does not depend from base you hire soldiers.
Also you can start training only for 11 rookie soldiers - the training button for 12th soldier simply not highlighted and could not pressed by mouse button instead this the "not assigned/chinook01" menu appeared.