Steps to reproduce on my PC.
0) INVENTORY HAD PLENTY OF EMPTY SPACES.
1) Mine granite
2) with an odd number of granite pieces, place ALL in mini-crafting (e.g. no crafting table)
3) Craft polished granite - 1 to 3 pieces left over. Use the SHIFT button to craft as many as possible that go straight to inventory
4) Press E to leave inventory. The 1 to 3 pieces drop to ground.
5) pick up the 1 to three pieces and check inventory. Polished granite is not there.
6) exit game and restart. Polished granite is in inventory.
NOTE, once I exit and return I cannot reproduce this bug. Yet, I carefully reproduced it several times until the exit, restart.
Obviously a low priority bug, given the now inability to reproduce.
Just and FYI
Inventory was 1/3 full, not completely full. The overflow, however, could have been that the use of the shift overflowed ONE position in the inventory past 64. However, the inventory itself had plenty of room and the ENTIRE STACK of the granite disappeared (normally, the overflow I would expect to disappear).