Similar issue, only buckets were in inventory and using them dissappeared.
"While using the Powered Crafting Table to take one bucket of water to double it. Upon doing so(1 bucket of water + Empty bucket) you get 2 buckets of water stacked. Using said water bucket in it’s stacked form causes the 2nd bucket to disappear leaving only 1 empty bucket in inventory.
Current Fix: Unstack the water buckets in inventory and then it works as intended."