This happens to me nearly every carrer after a number of 'sucessfull' mission.
What makes it even more frustrating is that all those passive skills will push those with active skills 'off the page' so the actives cannot be selected
So the only alternative is to say 'Good job sailor' and send them on there way. In other words trade them out for unskilled sailors while in port.
Im runnng RFB+RSRD btw.