Industry completes a good. It now has a vacancy. SY sees vacancy, sends out a delivering cartpusher. While the SY cartpusher is en route, a cart from a raw material supplier also sees vacancy, and fills it before SY cart arrives. SY cart arrives at the now full factory...and it goes inside. SY cart then disappears from view until industry completes its current good, at which point the SY cart delivers raw material and returns to SY.
This means that a SY cart, delivering raw materials, can disappear inside an industry for slightly over two months (the time it takes to manufacture a product). Raw material producer carts don't seem to suffer from this problem.
Possible solutions:
Delete/undo on the SY frees up the cart. This means micromanaging and is a serious pain. It also deletes the raw material the cart was waiting to deliver.
When an industry is supplied both by SY and raw materials suppliers, count on the SY to have significantly reduced delivery/getting capacity.
Isolate road networks, creating manufacturing districts which have sufficient local supply of the raw material (and those don't need a delivering SY). If you also want to export the raw material, create an isolated area for production and storage in SY. This solution will often mean wasting some raw material production, but might often be the easiest to manage.
I've only observed this in a single city, but I suspect it's been the cause of some strange interruptions in SY operations that I've noticed in other cities. Who knows? Anything is possible.
-- JWorth