Okay, I hate to be the one to spill this nice exploit, but instability of the weapons tray (both ground and space) has done it in.
On various shuttles, ships, and freighters, I am getting additional weapon effects from my other Bridge Officers. Sometimes, I get them from the assigned Bridge Officers. Example, in an Lt. slot, I get Commander abilities as well.
As much as I hate to see this reversed, the weapons tray keeps resetting itself. When I assign an effect on a specific slot, it disappears when I change characters and come back or leave my account and come back.