In my most recent game, I had a tremendous number of item stacks in the Missiles and Wands category. However, when I decided to manage my inventory with the comfortable drop command (or whichever command it is that allows you to specify any number of specific item stacks to drop), I noticed that some of the items stayed in my inventory even after I carefully double-checked enough times to be absolutely sure I didn't just miss/forget the unwanted items on the first few passes. Looking at the floor contents, I found that several items I wished to keep were now on the ground. Only wands and missiles were affected in this manner, while other item types which I had fewer varieties of, such as potions and scrolls, did not encounter this problem. If I properly recall, the comfortable drop command seemed to drop the wrong item about a quarter of the time, but that might vary depending on the number of stacks in the category, number of unique stacks in the same category selected, and my failing memory.

Sorry about the lack of tags; I accidentally hit some button combination that prematurely submitted the post.