I couldn't find another topic about this, so if it's been mentioned already I apologize.
The long paragraph is me simply explaining in detail what I was doing/did to make it happen
This afternoon I was swapping around weapons and items on my ship and I noticed that nothing was moving when I moved them so I figured it was just some hardcore lag. 10 seconds later; "Lost connection to server" came up on my screen(or whatever the red lettered message is). The lag eventually fixed itself and the items all went to where they were supposed too, except for the fact that the phasers went into the console slots instead of the weapon slots. I had fully functional phaser banks in my engineer console and tactical console slots. It also placed two new fire phaser buttons on my skill bar. They also worked in combat. I took one out and tried putting it back in but no dice, now I get the "does not go there" message. So I'm currently flying around in a bugged three weapon ship(four counting torpedos).
I'd post some screenshots to prove Im not crazy but I'm writing this from work.