I can find old threads of this happening (2015) but didn't find any newer reports, though I may not have searched the correct string so if this exists in a report all ready, I'm sorry.

If my chest is full and I shift+click something into it, my items just disappear forever. I lost my diamonds this way when I was putting the stack back and opened the wrong chest which happened to be full.
I tried with some sticks and things like that, and sure enough, you can repeat this bug.