I have the same problem of items either this (above^), or not stacking properly (sometimes I'll look down and have 3 or 4 stacks of coal of 2, 5, 36, and 87, generally speaking. The only way to fix it is by throwing out all the items, or at least all but one stack, but this is a massive hassle when the first stack (and thus, the one it throws from) is the one with 87 items. :/
The stacks are super glitchy, and this is an important bug that needs to be fixed.