Issue
Placing buckets into a tank containg less than one thousand(1000)mb of liquid will delete up to two(2) buckets. if an empty bottle is in the tank output slot, and removed after placing the bucket stack, up to three(3) will be removed.

repro steps
place water bottle into tank
place stack of buckets into same tank
remove glass bottle
pick up remaining buckets and place back into tank
lose five(5) buckets total

In my case water buckets and water bottles are not filling the same tank, because it's different type of liquid (as it should be)