With build v 5.7c when using a crafting station, if you attempt to use the pestle item and powder pouch in the grid, with any amount of a Roots herb (excluding most seeds) there are a series of odd interactions.

Items used to craft while in the crafting station are not used, in spite of the item result being created. If the pestle is in the upper right left hand most corner*, the bag will be duplicated; and the item can be shift-clicked to create additional duplicates at the same time, again without expending the items intended as consumable. This issue however does not seem to extend to the vanilla crafting table but it is worth considering interactions with other blocks that allow crafting in a 3x3 grid.

The glitch should be reproducible in both creative and survival modes.

*If the pestle is in any other location, the bag will be duplicated only once, and a pestle will be generated in recipe. Typically in the upper left most square.

The duplication seems to still occur in the crafting station (in both in and out of creative), though not even using the traditional crafting grid will combining moss in any amount with - a new - pouch and pestle, fill the pouch for the necessary roots staff functions. Previously existing pouches (from worlds created pre-5.8) fill as per-normal, with the duplication glitch in the crafting station still present.

Can you try this in v5.8 please?

If this is a different bug I apologize, but it sounds like what I was experiencing:

This occurs with many items and is not limited to Roots. The intended Elytra dupe gives me two of my original Elytra along with the new one. Creating Mana Dust duplicated my Petal Dust (was I even supposed to get that back?) instead of consuming. Creating an Anima Mundi gave me two Mana Dust back (was I even supposed to get 1 back again?). I think those are the only cases I had dupe like that.

All of the above crafting was done in the Refined Storage Crafting Grid, manually.

I can confirm an instance of it happening in 5.8 (I think my previous comment was in 5.8, but I couldn't quite remember). In this case I got 2 Schwarzenegger Spheres when I crafted the Unified Field Core.

EDIT: Crafting a Super Worm gives me back 2 ATM Stars.

@nullKomplex yes the Refined Storage Crafting Grid duplication is most likely another bug.
We also have the duplication of returned components in RS Grids. I think it's related to
refinedmods/refinedstorage#1685
Which should be fixed in the newest version.

Please update to latest version 5.9.2