Had similar trouble, trained one of my BOs another Ensign skill, but he ended up having his old and the new one. Messed up his LtC skill for me as well (icon for LtC skill did not show in space HUD).
What worked for me: I retrained one of the Ensign skills and this way my BO got rid of his 2nd Ensign skill and the LtC skill worked fine afterwards. And the Ensign skill i retrained had already 9 skills points on it, they stayed, so you I did not lose training when I retrained.
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What worked for me: I retrained one of the Ensign skills and this way my BO got rid of his 2nd Ensign skill and the LtC skill worked fine afterwards. And the Ensign skill i retrained had already 9 skills points on it, they stayed, so you I did not lose training when I retrained.
Maybe this works for you as well, good luck : )