After the mission the doomsday device I can't use some of my bridge officer skills like torpedo spread and attack patern beta II.
Does anyone know why this happend?

You need to re-arrange your stations and toolbar. Being in the BOP messes with your setup.

I've found that when you return to your normal ship, after the mission is completed, placing your bridge officers in the exact stations you had them seated before the ship change to the Klingon Bird of Prey, re-assembles your toolbar as it was before the mission, for the most part.

This only seems to work if you haven't tried to re-populate the whole toolbar already. Hope this little trick helps.

Cheers