Yea the raw mats returning is a known issue, we are working to only give you the refined material back.
Thank you. Thank you. Thank you.
For this iteration of the game, Beta after the wipe, I chose to have one of my characters be only a harvester and one be a crafter. They are Forester and Prospector, and Provisioner and Weaponsmith respectively.
When I deconstruct on the crafter, I'm forced to restack the raw mats, put them in the bank, then log to my gatherer to reprocess them. Put those in the bank and relog back to the crafter to use them.
In earlier iterations of the game I'd paired one gathering skill with the most logical, in my mind, crafting skill, thus eliminating the above problem for the most part.
What I'm rambling on about, errrr saying is it just makes more sense to deconstruct into processed materials rather than raw materials. The deconstructed items were made from processed materials NOT from raw materials directly. Cheers!