Over the past month or 2 of playing I've had stacks duplicate maybe 10-15 times (so not that frequent but frequent enough to notice). Every time it was when using pick block on something I already had a stack of in my inventory (but not my hotbar). The stack came to my hotbar as expected, no ghost item problems, no stack count changes, no problems at all. But when I went to put it back in my inventory it was already there. The one in the hotbar was a duplicate. Taking both stacks (eg: 19 stone each) and merging them works with no problems (eg result: 38 stone).
And yes, I searched for duplicates of this bug first (using "duplication pick block" and "pick block duplication" as my search terms) and none of the results were the same bug.