e.g. needed resources being deposited in silos (or dithering in and out of them) can be cause by having 2 or more refineries on the same line, or multiple different routes resources could take (dependant on being raw/refined). This can also cause bypassing, potentially.
Refineries may also skip a beat (if not setup up very specifically) if they try to refine more than 5 chunks in a row. The classic crafting bug. Plus other more subtle issues in guide.