At least it was only 10k. You sure you didn't spend it on reps/items/zen/fleet holdings?
NO. I didnt, cuz even if i did that, i should have some dilithium, not 0, i dunno if you know what i mean. I never waste all my dilitium, at least it was not the dilithium ore (i have about 60000 dilithium ore..=.
I just hope this not happen again, or i will reach my limit playing this game.. xD against all the bugs.
I have never heard of a lost dillithium bug. Go to the dilithium exchange and check your exchange log. If there is a transaction over the mission amount your account has been hacked. If there is no such transaction it is very likely that you have spent it. Alternatively something could have hacked the account and spent if for you albeit I think that's very unlikely. Even more unlikely however is a bug making your dill go boom.