I had the same problem today. I have 4 Elite, 4 Advanced, and 3 Standard - I have a total of 6 items out of them. Some worked, some didn't - I have 1 Elite worked, 2 Advanced, and 2 Standard. (not quite sure exactly).
But yes I think there must be a bug. They had this bug in the Tribble test system, however I hadn't seen it in Holodeck until now.
I have opened 4 boxes which I got from the hard missions, 2 vanished, nothing in them. Later I bought 15 boxes from the exchange at 350K each, out of 15 boxes only 9 opened. Cryptic you owe me some EC. SUCKS BIG TIME. I am not going to open any more boxes or run these missions again until this is fixed!