Cotton fever is a terrible thing. Anyone using intravenous drugs should do every thing they can to avoid this experience. Since you must use cotton as a filter, it is always a hazard, but there are precautions you can take. When using heat to break down the drug, let the solution cool down before dropping the cotton in, and never apply direct heat while the cotton is in the solution.
Heat frees up and breaks the cotton down so it is more easily sucked up into the syringe. Sometimes people save a number of cottons from each use, and mix them with with water when they dont have other drugs, especially with opiates and a daily physical addiction. This is very dangerous, especially when heated with a lighter in a spoon. (I caught the fever this way)