I found bug, which destroys all but one item if you remove huge amounts of something from the shop.
For example I added like 5000 muhsrooms to my shop. And when I removed them and same time a stack of wool, all wools but one dissappeared. There still were those 5000 mushrooms. This has happened twice to me.
Any idea why?

It's a control as removing large amounts from a shop will crash your server. Notice the other issue about removing large amounts already on the issue tracker?