Was Master Looter on? It's a pretty well documented issue at this point that using ML screws up loot.
Leave group loot on, have you raid leader right click an item one at a time to bring up the need greed window, figure out who gets it, etc. If you're with half decent/intelligent raiders, you can do it this way.
Simply leave it on group loot. Have raid leader be the first person to loot the boss/chest. The leader can say what is on the boss, you can figure out who gets what. The loot than right clicks an item from loot window, and the group gets the need/greed window. The previously decided person needs, everyone else passes, loot goes out.
It takes a little longer and is tedious, but it also seems to mean you always get the correct loot.
That's fine, most guilds probably did as well. Ours definitely did, and we were annoyed by this mechanic as some items certainly went to the incorrect AC, so the next week, we did HM. I know it sounds like people saying what you should/shouldn't do, but they are just pointing you in the direction of a solution to your problem. The step up from normal to HM is extremely small, and if you handled normal with ease as most guilds do, you'll find it more enjoyable. You'll get gear handed out to the correct players via master looter.
Provided master looter bug doesn't show up so you only get schems and exotech.