Many of my Siddurim have a version of Hamapil that’s not the same as the one given in Brachos 60b. Others have the version found in that Gemara.
Where, and why, does the variant version come from?
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I believe that you may have been misled by the fact that nowadays most rely primarily on the Vilna/Romm Shas. However of the different manuscripts of Berakhoth 60b and commentaries thereon that have existed over the centuries, different versions of this prayer have been presented. The printing of the text and its widespread adoption led to the many variants falling to the wayside and often forgotten about (see the Diqduqe Sofrim, vol. 1, p. 345). R. Drew Kaplan describes the varied nature of the nusah of ha-mapil as found in manuscript as follows (Birkat Ha-Mapil: The Rabbinic Pre-Sleep Blessing, p. 160):
While the opening and concluding lines of the blessing remain more or less consistent throughout the various texts, the middle sets of requests differ widely. A number of possibilities account for these different versions. There may have been initially a shorter version upon which people added lines, or a longer form which became shortened. Alternatively, it may have been a medium-length blessing with various strophes being added and/or deleted.
As @magicker72 notes in the comments above, the text of the Gemara, especially as regards the nusah for blessings and prayers, was often edited to reflect the local practice.
As for how such differences in nusah developed between communities in the first place. That is primarily a function of time and geography and sometimes competing halakhic traditions (e.g. Babylonian vs Israel based practice). As well as the halakhic culture of different communities historically, with some being more open to overtly adapting/modifying the nusah and others being far more conservative and averse to such change (if I recall correct, this was once a bone of contention between French and German Jews, I'll cite to Kanarfogel if I remember later).