Quote of CraftySubZero
"Im not sure if this bug has been previously mentioned. But, when a player shift clicks an item into his inventory. If all other slots are taken, the items will be pushed into a slot containing the same items, but it will overide the stack limit for that specific item. Hopefully that makes sense :)

If the items remaining after exceeding the limit (Upon shift clicking) could be dropped onto the floor or something, that would be great."

This appears to be fixed in 0.9.4. Any items that don't fit stay where they were.