It seems to happen randomly but I notice it in the middle of progressing to high arena waves when the game is left open for a very long time. This time around I have screen shots that might be helpful.
Using windows 7.
As you can see my glancing blow affix shards are at -1. I used more than one glancing blow affix shards while crafting in this case even though the displayed glancing blow shards was only one. Thus leaving the negative value.
This is just an example of a variety of affix shards that have a value of 1 despite having many more than that. Along with the -1 for glancing blow.
Basically if I keep the crafting window open I can keep crafting beyond the 1 count despite the listed value being 1. But if I close the crafting window after using the “1” affix shard the game thinks I have it will disappear from the list until I find another one.