Like Game said, there's usually a hidden reason behind why an item disappears.
Usually during a lag spike, you may have picked it up by accident and drop it without knowing.
Or I believe if you're killed enough and cause too many bodies to pile up you can possibly lose something.
Or possibly even a roll back of the server but I don't see that happening very often or at all really.
Possibly many other reasons for why it could happen, but surely not items disappearing out of thin air.