Pirkei Avot seems to have several versions- -both the numbering and the actual mishnayot differ from Sefer to Sefer- for example the standard printing with the commentary of Rabbenu Yona differs from Kahati in some places, and from the Artscroll in others. I assume this is not the norm with other mishnayot.
It is very common for there to be different divisions among mishnayot. Originally, the mishnayot were learned as entire chapters, and one can often see the Talmud or Talmud Y’rushalmi divide the mishnayot within the chapter, differently than in the different editions of the printed mishnayot or Talmudim. With Love of Israel! Rav Ari Shvat