And if this isn't the case... tough titties. GM's really don't give half a $#!+ about your problems.
Missing non-existing items in a computer game, yeah, these are problems.
their title is GAME master.... so this would typically fall under GM problems... at least we'd hope they would...But you know, the game is in Alpha, and the title of GM is "person with special powers the residents of NCR will flock to when they appear"
There is not much GM can do to find out what happened, and if it was a thief,GM couldn't tell it anyway, because it would be unfair for the thief.
A little sleuthing has revealed the crafted containers can be stolen when they are empty if you use the science skill. I also suspect a certain someone, so it is no longer any issue to me as they have been expelled.