In the Siddur, Pirkei Avos has a different division (in each Perek the amount of Mishnayos) than in the Mishnayos Avos. Who determined the division of the Mishnayos in the Siddur?
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It seems to me that there is no canonical division of mishnayos beyond the level of perek.
My basis for the statement is the way the Gemara handles and speaks of the mishnayos. In the Gemara, the division of the mishnayos is based only on the discussion. At times (ex. the third chapter of Taanis, starting on 18b) the Gemara will have the entire perek of mishnayos as one undifferentiated lump at the begging of the perek, followed by the Gemara. The term 'מתניתין' - "our Mishnah" - is always used to refer to the entire perek, including teachings that are found later.