I am playing 0.4.13. I haven't even set up burrows.
EDIT: I think it has something to do with dwarves moving the whole bin to continue storage labors, I'm not sure if they move the whole bin when they need one of the strands for creating wafers or cloth.
Dwarves have always done this. Pretty much ever since bins were introduced.
You can stage things so that dwarves take them out of bins a few at a time onto a small stockpile so that bin shenanigans are less of a problem.
Does it apply for production, storage or both?. I find it strange, my blue candy stuff production is usually a lot less complicated.
It's most problematic with bins that can store a lot of items that get used for other things. In this case, a thread bin is kind of a horrible thing if you have a textile industry or web collection running. In fact, you might be able to nip this whole thing in the bud by disabling your loom and farming workshops while you do stuff with the adamantine. Otherwise, the bin will keep getting grabbed to pick-up textiles as they get finished.
Let's use rope reed as an example.
Rope reed is processed at a farmer's shop into thread. Somebody comes and grabs a bin with some room in it (in this case the same that have all your fibers in it) and run and go collect the thread. Now, the bin already has a lot of stuff in it, so it's pretty heavy. It takes them a while to drag the bin to the thread they're picking up and drag it back. All the while, all the fiber-jobs are canceled because the bin isn't accessible (somebody else has it). Meanwhile, other textile jobs are getting done that produce more thread and cloth. The bin eventually makes it back to the stockpile, but with all the other textile jobs, it's almost immediately grabbed for another hauling task and dragged off. By the time somebody gets around to trying to do a fiber job, the bin is gone again.
This is exacerbated by the fact that you can store a TON of thread in a single bin, so it'll bottleneck any job that needs something that's in that bin.
This can be solved in a number of ways. First, don't use bins, or only use them for finished goods you intend to trade away or other low-use goods. You can get around the need for bins with comprehensive minecart quantum stockpiles.
Second, you can create infeed and outfeed piles. These are piles with bins disabled that are designed to stage your materials.
For example:
You have 3 stockpiles: Infeed, holding, and outfeed.
The infeed pile is set to take from anywhere, has bins disabled, and is relatively small. Haulers will drop off cloth and thread to this stockpile without using a bin. This stockpile is set to give to the holding stockpile.
The holding pile has bins and can be however big you want. This is set to take from links only, so it will only ever take from the infeed pile. Workers will grab bins and move to the infeed pile and pick things up. This pile is set to give to the outfeed pile (or piles).
The outfeed pile is typically targeted to a more narrow selection of goods from the holding pile (for instance, adamantine fiber) and will be fairly small say 2x2 or 3x3 and placed near the crafting workshop where the stuff will be made. Haulers will pick up the items from the holding pile to try to keep the outfeed pile stocked.
My preference is quantum piles, or specifically targetted piles for certain applications (like a special pile to hold my adamantine). 3-stage piles are good for what they are, but they require quite a bit more labor than QSPs. Pretty much I use multi-stage piles most when I'm doing a lot of plant gathering. Using a feeder pile, I can force the gatherers to use a stockpile with barrels disabled, keeping them from dragging a barrel out to the surface and back just to get a handful of berries.
QSPs have the added benefit of improving FPS a bit, so they're usually my choice of management strategy.