Edit by [Minecraft] Mega_Spud (Jay Wells):
It appears that this issue can occur when interacting with other block entity/NPC/Mob inventories, including Villagers.
In my survival game, there are times when items disappear from my inventory. I have tried to find when and where this happens, as it has occurred very frequently.
And I found it occurs when I have been exiting my mine, with all my resources, I go to a series of furnaces that I have to make cobblestone into stone. And whilst I'm putting more wood and cobblestone into each one. I notice after that some items are missing.
The missing items that I have noticed, have been torches and also iron ore.
I usually always have my torches in the second slot, if this is related I don't know.
However they have definitely disappeared as I kept an eye for it this time.
I'm pretty certain it has something to do with the furnaces. Wether it's because I have 8 furnaces in a 2 by 4 set up, or the fact that I fill them up and take out the stone multiple times, I'm not sure.
However, please try find and fix this.
If it helps the slot torches were in, had been replaced with stone. So it must occur when I'm taking some out.
I have version 16.2 minecraft pocket edition.