You can also set up stockpile links. Set your main stockpile near the depot to "take from links only" (default "a" when looking at it with "q"). Then set up another stockpile that also only takes from links, and link it to the craft shop(s) you make all your crafts out of. Then select the second to give to the first. Crafts should go into the stockpile near the workshop, then get carted to the one by the Depot. So long as you don't make any other finished goods out of htat workshop, nothing else will get mixed up in it.
More simply, you could just adjust the material/item settings as previously mentioned. Oddly, all the -specific- random crafts can be toggled on/off, but we get this catchall "tools" section to toggle all or nothing. That tool section includes things like instruments and instrument parts as well as book bindings/scroll rollers. It'd probably be easier to just turn off things like tools (that can also be made from stone) while only allowing materials made from stone.
We really do need a stockpile overhaul... I have to use the complicated linking assignments above to separate the instrument parts and book bindings from the rest, then send the book bindings by the jewelers workshop to decorate them before sending them back near the library and its craftshop (that needs a similar set up to only accept sheets and quires...) Craftshops are a little too universal too- I have 5+ of them spread throughout my fortress, and can't queue up manager jobs for them. As the manager just adds 9 bone gauntlet jobs behind my stone-only workshop set to repeat, or forces my woodcrafter to carry wood past THAT craftshop all the way down to where the bone shop is.... or just gives me massive cancelation spam when I have links set up for the wrong material.