i'm sure there are people who know more than i about this, but to start off, emma called herself an anarcho-communist, whereas voltairine didn't hyphenate (ie, she supported anarchist thinking of all sorts).
i have never read anything specific about their disagreements, but there seems to be divergent emphases... like emma is famous for being pro-free love, while voltairine wrote about being anti-marriage. emma supported violence, whereas voltairine forgave violent people... (and emma was of course an extremely public figure, famous for her presence and oratory, whereas voltairine was more private.)
i hope a historian or two weighs in on this. i'd love to know more about this myself.