So a lot of people know about the autofire bug or have encountered it.
Many more people also know of the unassignable BoFFs bug.

These bugs may typically occur when switching to a newly-obtained ship, but may also occur at other times as well.

So here's the solution:

-Autofire Bug
--Go to Sector Space.
--Hit Escape, go to Options and then Rearrange HUD, find the panel that says 'Ship Weapons', make sure it isn't orange/hidden, then hit Escape again.
--Right click the weapons on that panel and your AutoFire will be working again, this is a workaround that can be used in the meantime.

-BoFFs (Bridge Officers) can't be assigned to stations
--Switch to the previous ship you were using
--Remove all BoFFs from their stations
--Switch back to your new ship then try reassigning them to the station, it should work this time.
--If not, try switching back to your old ship, make sure the stations aren't assigned, then completely exit the game and relaunch it. Repeat the first 3 steps and it should work.
--If not, dunno how to help ya Go bug Cryptic/PWE.

is there a solution when you own only one ship?
it is the case for my kligon (just starting it)

There is no panel in the Options menu that says "Ship Weapons"....So you must mean "Rearrange HUD" ....and by the way...it didn't work for me. Still not able to deselect or select autofire

Found it under Rearrange HUD not options (as mentioned above) but the fix did work for me, thank you!

Added in the Rearrange HUD thing. I kinda wrote this out really quick and should've proofread it.

If you right click on your Ship Weapons while you are in SECTOR SPACE (you should see a disable astrometrics button somewhere on your UI) then this should work.

I've added both of these to the first post.

Well for your Klingon character I don't know. If you just started it then try the suggestion in the first post. If it doesn't work for you then you might have to wait until your first ship upgrade (or buy a ship with Zen?).

There have been scattered reports of some bugs when using the 'switch character' function so you might wanna completely close the game, reopen it, then login to your Klingon and try it again. Ignore the 'change character' thing if you're changing to a different faction character.

If none of that works then just remake your Klingon and don't use switch character in the future.

Found the temp fix.....change the space tray back to "1" layout...you can then add or disable autofire. Then change your layout back to 2,3..whatever you want.