some cigarette filters aren't 100% cotton or even cotton at all....particularly those little "cheap cigarillos", I'd never use those...I don't use cigarettes filter cotton unless nothing else is available, I always heard that "camels" are 100% cotton and the best filters to use if you use cigarette filters at all, not sure about that, I could probably verify it with a search.....
Cotton fever sucks, it's always happened to me when I least suspected it was gonna happen.....I always thought it was from "little pieces of cotton", but there's a lot of web sources that say it's from a bacteria that grows on cotton...there's a lot of conflicting info on this...IMO, there's several things that can cause the same reaction ranging from what the drugs are cut with to bacteria to IVing particulate matter...I've had batches of dope that gave cotton fever to everyone who used it and other situations where the evidence pointed to things other than the filter itself...
As always, the only thing you can do is use clean equipment every single time, and even then, IV heroin is not exactly a "safe" hobby, but aside from ODing and missing shots, the majority of negative consequences related to IV heroin come from lack of cleanliness...