Well, there are only a few possibilities for such a scenario.
Get more (qualified) crew into the compartment and an officer too.
Make sure silent running is off - reestablish SR and then switch back again.
Check the 3D situation for the tubes. Switches at the WEPS station clear? F12 to the outside and check the tube caps to be closed.
Do you play with sabotage/malfunctions on?
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