This is most likely because I'm playing with a certain combination of mods and the refinery speed is way above normal.
So, when an item enters the refinery and there is not enough slurry in the refinery to upgrade the item, it can get stuck and even when the slurry reaches the required amount, the item will not be upgraded and will stall the refinery.
This mostly happens with items that need the maximum amount of slurry for refinement that the refinery can hold (1.2k).
This also happened a lot before when my slurry production wasn't producing enough and even items that didn't need much got stuck.
It might be solved with doubling the internal slurry storage (that last percentage of slurry takes the longest to fill up) or by having it recheck if there is an item inside together with the required amount of slurry I'm guessing.
If you'd like to take a look at my save file you can send me a message on discord where I go by the same username as on here.