Hi there,
This isn't necessarily a bug but maybe something that was just overlooked when the Herb Bags were introduced.
When you go to craft at the Alchemy Station, and you have your plant material stored in a Herb Bag, it will show you have the plant material available to use but when you press the Craft button it won't craft the potion. Once you remove the plant material from the Herb Bag and have it in your normal inventory space it works just fine as it should.
On a side note, items won't stack automatically within the new containers when you drag and drop them in from within the inventory. Instead they take up another slot as a separate stack. It would be good if they automatically stacked.