That "example" -- Ben Meir and Israel vs R' Saadia Gaon, the Gaonate, and Babylonia is the only such dispute over the calendar.
I "published" on Avodah a copy of an article by R' Yosef Gavriel Bechhofer and R/Dr Ari Z Zevetofsky at Avodah v5n35 #8: Calendar Controversy Article. They propose an interesting possibility for the cause of the dispute.
You ask about what people did in practice. This actually threatened to split rabbinic Judaism, as Jews in Israel were following Ben Meir over R' Saadia Gaon. Realize that this is before Talmud Bavli became "The Gemara", at least in the eyes of the community whose ancestors were taught by the amoraim of Israel, as recorded in the Talmud Yerushalmi. It was also at a time when Qaraism was new and upsurgant.
Thus the heat of the battle was more over the unification of rabbinic Judaism under the gemara than the actual calendar issue itself. This trend then continues into Ashkenaz, where much Eretz Yisrael practice co-existed with Babylonian rulings. (At least according to the dominant theory in the history of halakhah.) And now that the the gemara and geonim gained universal acceptance they had to find an understanding of halakhah that includes both the babylonian texts and practices that come from a wider variety of sources. And by the end of a couple centuries, the challenges yield the schools of Tosafists.