Ok.. I didnt know it when i 1st started the game, but did find out about it much later.. Theres a bug, that causes items in containers to appear invisible.. If you use the spacebar, or click "loot all" on the containers, it will loot the invisible items, and they do appear in your inventory normally..
This neds to be patched, as many, like myself, missed out on every single piece of loot in containers.. Luckily, i found out about it before leaving Cyseal, but i had to go back to every place i could remember, and loot.. Not to mention, i just lost my entire saturday,, trying to find out what the problem was, and come up with a solution.. This problem has been reported since day 1 (according to some posts ive been able to find), it should be patched immediately!
TLDR: Its invisible loot.. Use the Loot All function, and they appear in inventory.. Definite BUG