I have had this happen as well. Looking at loot drop lists and what I kill, combined with the battle/chat log I think I have a good answer. When you kill a mob, sometimes you will get the skill/exp for said kill, but no loot. Walk around, go to an area with less lag or even more people and the server hickups a little. You will see your loot come.
Example: I killed a marmot based animal, went to one of the main cities and then it said I received Marmot meat +1, and a few crystals. This took me about 5 minutes to get to town and load, I knew where it came from because that was my last kill.