When the Mishnayos were compiled, were they compiled into the perakim we have today, or were they just compiled into masechtos?

Question

Many times throughout Shas, it seems as if the Perakim are sliced in completely arbitrary places. To name a few examples:

In Maseches Shabbos, the halachos of Tzad, trapping, are discussed in 13:5-14:1. It seems odd that the last Mishnah regarding trapping is attached to the following chapter rather than having all of the halachos of trapping in the same chapter.

Further on, Muktzeh is discussed in 17:1-18:2. Why not attach those two Mishnayos to chapter 17? The third and final Mishnah in chapter 18 discusses helping animals and women give birth on Shabbos, and what one may do with the baby afterwards. These prohibitions and permissions, according to Rashi to Shabbos 128b, relate to the prohibition against doing extra work on Shabbos and the permission to do whatever is necessary to save a person’s life. These have nothing to do with Muktzeh, but this Mishnah is the springboard with which the Mishnah justifies the following chapter being about what acts of Bris Milah may be done on Shabbos. Based on that, it would make more sense that it start chapter 19, rather than conclude chapter 18, which it doesn’t have anything to do with.

Another example from an entirely different masechta: Rosh HaShanah 1:3-3:1 discusses the witnesses’ testimony for Rosh Chodesh, and the procedure done once their testimony was accepted. 3:2 picks up with the halachos of Shofaros, discussed through the end of the masechta. Why is 3:1 not the end of chapter 2?

For one final example: Bava Metzi’a 7:1-8 talks about someone hired to watch produce. In the middle of Mishnah 8, the Mishnah switches to talk about general halachos of Shomrim, which it continues through Mishnah 10 (with a slight tangent in Mishnah 11). In chapter 8, the Mishnayos continue with halachos of shomrim. Why is the end of chapter 7 not prepended to chapter 8?

There are many more examples I could bring of these types of scenarios. While the order of Mishnayos within a masechta are in order (Avodah Zarah 7a), can one deduce from such scenarios as the ones above that the perakim were a later, perhaps arbitrary decision? Especially in light of the example in Bava Metzi’a, perhaps one could extend this argument to where the Mishnayos begin and end.

I am not asking for an explanation for these particular cases. I am asking if anyone says explicitly that the perakim in Mishnayos were a later addition or not. If the answer turns out to be negative, perhaps I’ll ask that separately.

Answer 1

The 1906 Jewish Encyclopedia answers that the division of the several treatises into chapters as well as the sequence of these chapters was the work of Rabbi [Yehuda HaNasi] himself although some changes were made over time. See there for full references.

The division of the several treatises into chapters as well as the sequence of these chapters was the work of Rabbi himself (Letter of Sherira Gaon, l.c. p. 13). The portion discussed each day constituted an independent pereḳ; and this term was, therefore, applied elsewhere to a single discourse also. Generally speaking, the original division and sequence of the chapters have been preserved, as appears from various passages of the Talmud (R. H. 31b; Suk. 22b; Yeb. 9a; Ket. 15a; Niddah 68b; Zeb. 15a).

The names of the chapters taken from the initial letters are likewise old, and some of them are mentioned even in the Talmud (B. M. 35a; Niddah 48a). In the course of time, however, various changes were made in the division, sequence, and names of the chapters; thus, for example, the division of Tamid into seven chapters is not the original one. On other variations in sequence see Frankel, l.c. pp. 264-265, and on the changes in the names see Berliner in "Ha-Misderonah," i. 40b.

See also the Rambam's introduction to the Mishna 15:15 where he writes

Afterward, [R Yehuda Hanasi] divided the material that is in each of the specific categories into sections and he called each one, chapter. And afterward, he divided the material of each chapter into small sections that are clear to understand and easy to know by heart and to teach, and he called the name of each one of these small sections, law (halacha [more commonly referred to as mishnah]).

I remain puzzled about the logic for cutting chapters this way and don't yet understand the rules used.