I was wondering that too. I rarely sort my own reagent bank tbh. I’ll run through some permutations this weekend to see what might be the actual trigger here.
I really think it has something to do with realm hopping though.
Edit: 8/17
I unfortunately couldn’t catch it in the act, but of course it did it again. I was playing my Horde mage on Uldaman through to 70 doing the echoes… didn’t notice anything missing. Logged into my Alliance rogue on Gnomeregan - boom - 3 things missing.
These weren’t that important but the concern remains. The war bank will eat your items. I even tried recording a session Thursday evening but nothing went missing no matter how much I used it.
Hey Blizzard, do you think this might happen when the war bank sees more use across players? I think you have a problem but I can only tell you what is happening to me. Others may not be so astute in what’s stored in their war banks.
Edit: 8/17 - CAUGHT IT!
Alrighty! I caught it in the act. I have a video to share for it too 
https://youtu.be/ry7WSrbrvD4