I got alot of ships with -%, usaly 7-10% and can´t train it away... It come as soon as I build them I think...
Is it a bad commanders, to small crews or what??
You have a pool of trained personel from your acadamies, this pool consists of crew with a training of 0 (This can be changed) when you run out of crew from this pool new crew have a rating of -10% (A ship with a mixture of these conscripts and trained crew has a range of -1 to -10%). However this penalty can be trained out, to do this place an officer in charge of the ship with a crew training rating and wait eventually he will give the crew a positive bonus until that reaches its cap. To save trained crew you can set your some ships to automatically ahve a cosncript crew typically civilian ships like freighters where the crew grade is not important, this is done on the ship design screen.
This should really be in the acadamies section.