There are some isues losing items partly or complete with removing Crafting Tables (Tier1-3 (maybe also Traincraft Table, i dont tested the traincraft table)) OR Caboose Wagons!
What happens:
Removing Crafting Tables (Tier1-3) --> if items are in the different slots for crafting a train you will lose parts of the items you put in if you remove the Table (example: you have put in 20 items of each you need, you remove the table and get back a part drop of for example 14 items of the one item and 12 or 18 of another, it seems some items randomly disappear here!)
Removing a caboose --> Furnance inventory gets lost (doesnt drop)

Your SKJ !

It does lose items partly (not all items get lost) only few items get lost from the workbenches...
For the caboose carts yes it completly loses invetories (furnance)

So, let me try and be clear on the issue you are stating, when you break a crafting table it doesn't drop the items it had in the slots.
Is that about right?
I think that was an old glitch from 1.6.4, don't remember if we ever dealt with it.

Off-topic: that's a good reminder though I need to deal with that in the rewrite...