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.