I've had a few users complain about finding empty crates in the mine shaft, and the mine carts outside. Lootable exists, you open it, no items at all. They can't show it to me of course though, as it disappears the moment they open it. Is it possible that the plugin isn't populating some crates and leaving them empty?

I am having no problems with mining crates that are inside or outside caves (all my bases are in caves) or the skips outside of the caves, while the players cannot show you an empty crate they can make a screen shot and make it public so that you can see it on their information page (if available) check your configuration for BetterLoot and any other loot plugin (if used)

I turned on container contents with admin radar, and found an example to show here. You'll notice the empty crate in front of me, and the one up above that has things in it.

there are a handful of simular threads that say the problem is you are trying to put to many items in the container, set it to max items 2 and see if you still have problems.