If you are crafting glass fiber from flint stones, and all of the flint stones are in 1 box and you break then they appear as a full stack and grayed out, if you log or zone they reappear as a full stack, I think that i may have accidentally duped a few stacks of flint stones, is there anything i'm supposed to do other than not continue using the bug?

Got that same problem, it sucks. I just craft by a zone.

It shouldn't be dupping any stones, what happens is auto-sort throws the remaining stones into another partial stack in your inventory and then that partial stack also becomes unusable. Pay attention to the numbers and if you actually are ending up with more than you should toss a PM to nasomi asap. Otherwise you should just be able to craft by a zone like shinbi said to avoid the problem. It happens with more than just flint stones unfortunately.