I'm also having some stacking issues. It seems random if I'm able to add sling stones into a stack or not. Sometimes they merge fine, other times they will not. I have about 6 individual sling stones in my inventory and two stacks that won't accept each other or the individual ones.
It also happens with potions. Are they supposed to stack? I'm pretty sure I stacked two reds at one point, but none of my greens will stack