I have no idea what causes it. Mine's a sealed system, with JG pex barrier pipe. The fact that the "flakes" (actually, they're more like crushed seashells) are black and magnetic means they must be iron, which must come from the radiators. But why they happen at all, and particularly why they line the inside of the rubber hoses ("crunchy hose syndrome") is a mystery to me.
My filter is a Spirotrap MB3. It does catch some flakes, but nowhere near as much as accumulates in the boiler and sticks to the inside of the rubber hoses. The system water is clear.
When clogged, the symptom I notice is the house taking longer to heat up in the morning. This is because the boiler is cycling to stop flow temperature exceeding setpoint, presumably because flow rate is so restricted.