Press the letter i key to bring up the torpedo loadout/inventory screen.
Look to be sure that there is a check mark next to AUTO LOADING in the upper left hand corner.
If Autoloading is off (unchecked), tubes can be loaded only manually by you. Spare eels will show as "in que awaiting loading".
You also need a weapons officer in the control room for loading to occur.
and remind Bernard to close the outer doors on the tubes before he opens the inner doors to reload.