Gemara

Version #1 (Shmuel): Any woman who had Bi'ah must wait three months before marrying someone else (to avoid doubts about who the father is if she will gave birth nine months later), except for a minor who converted or was freed from slavery. A minor Yisraelis must wait.

Shmuel already taught that a minor need not wait after doing Mi'un, but she must wait if she received a Get. Here he discusses when she was Mezanah.

Chachamim decreed that a minor must wait (after Zenus, even though she cannot be pregnant) lest an adult not wait.

Version #2 (Shmuel): Any woman who had Bi'ah must wait three months before marrying someone else, except for an adult who converted or was freed from slavery. A minor Yisraelis need not wait.

Shmuel teaches about after a minor had Zenus. Zenus is uncommon for a minor, so we do not decree due to an adult.

Question: Zenus is common for a convert or freed slave (before the conversion/freedom). We should decree!

Answer: Shmuel holds like R. Yosi:

(Beraisa - R. Yehudah): A girl who converted or was freed from captivity or from slavery must wait three months;

R. Yosi permits her to get engaged and married immediately.

(Rabah): R. Yosi holds that a woman that has Zenus uses a tuft to prevent pregnancy.

Question (Abaye): Granted, a convert intended to convert, and was careful (to avoid pregnancy three months beforehand) so she would know whether her child was conceived before or after conversion. A captive or freed slave would be careful if she heard from her master (that she will be freed or taken to a place where people will redeem her);

But if a slave went free because the master dismembered her tooth or eye, she did not know to be careful beforehand!

Suggestion: Perhaps R. Yosi agrees in such a case.

Rejection (Beraisa - R. Yehudah): A girl who was seduced or raped must wait three months;

R. Yosi permits her to be engaged or married immediately (even though she did not know beforehand to prepare a tuft)!

Answer (Abaye): R. Yosi holds that one who is raped turns over (after Bi'ah so the semen will fall out, to avoid pregnancy). R. Yehudah is concerned lest she did not turn over well.

Rishonim

Rif (10a) and Rosh (3:10): The Halachah follows R. Yosi against R. Yehudah, so one who was seduced or raped need not wait. Some say that the Halachah follows R. Yehudah. I do not know their source. Our Stam Mishnah is even like R. Yosi. R. Yosi permits only a woman who knows that she is Mezanah, for she turns over to avoid pregnancy. A Mishnah (41a) forbids any woman to get engaged or married within three months, even a virgin from Kidushin. Also this is even like R. Yosi, for it does not discuss Zenus.

Nimukei Yosef (Sof DH Tanya): Zenus, rape and enticement are not common (therefore, we do not decree about them).

Rosh (ibid.) and Ba'al ha'Ma'or: R. Meir is very stringent. He requires Havchanah even if she cannot give birth. The Halachah follows him against R. Yehudah, who is lenient in such cases. All the more so the Halachah does not follow R. Yosi, who is even more lenient! We follow the second version of Shmuel, which exempts from Havchanah only a minor who had Zenus, but not an adult. Shmuel holds like R. Yehudah, but not for his reason. Rather, Shmuel decrees Havchanah after Zenus lest one not wait after Nisu'in. Shmuel does not decree about Zenus of minors, for this is uncommon.

Rosh (ibid.): Regarding converts and freed slaves we do not decree about Zenus due to Nisu'in. However, we do require Havchanah if she converted from Nisu'in, even if her husband converted with her.

Korban Nesan'el (1,2): A convert should always be careful to distinguish whether the child was conceived before or after conversion. The Rosh holds that when a couple converts together, she is not careful, since in any case the child is from her husband. However, this is uncommon, so we do not decree about converts due to this case.

Rosh (ibid.): Shmuel did not mention a captive. Since she is a Yisraelis, we are stringent like R. Yehudah.

Ba'al ha'Ma'or: Rav Sheshes (Kesuvos 37a) says that we are stringent only if we saw that she was defiled. He holds that the Chazakah is that a captive was not defiled. We do not follow him, so we are stringent in any case.

Rif and Rosh (14a and 4:26): A convert and her husband must wait 90 days to distinguish whether the child was born before or after conversion.

Rambam (Hilchos Gerushin 11:21): A convert or freed slave must wait 90 days, even if her husband converted with her.

Magid Mishneh: This is when she was married before conversion or freedom. Even though a Nochris or Shifchah is Muchzekes to be Mezanah, one who is Mezanah is careful to avoid pregnancy. The Rambam holds that the argument is when she was not married, and he rules like R. Yosi, like Shmuel says in the second version. The Rambam did not mention a captive, for her Bi'ah is always Zenus (he already taught that she need not wait after Zenus). According to this, Havchanah for Yafes To'ar is only if she was married beforehand, even though the Yisrael's first Bi'ah with her was before conversion.

Rebuttal (Beis Yosef EH 13 DH v'Chosav Od): If so, the Rambam should have taught that a convert or freed slave that was not married need not wait! Rather, it seems that the Rambam holds like the Beraisa that (always) requires them to wait.

Mishneh l'Melech: The Tur says that a case occurred in which a pregnant woman converted with her husband. Some said that she must wait, for the Halachah follows R. Meir's decrees. It seems that she need not, for there is no concern for Takalah. Also, we decree primarily after divorce and Kidushin to another man, for this resembles cases when Havchanah is necessary.

Rambam (ibid.): The Torah requires a Yafes To'ar to wait 30 days for herself (to separate from idolatry), but she must wait 90 days in all for Havchanah.

Hagahos Maimoniyos (20): R. Shimon ben Elazar (Yevamos 48b) expounds that she must wait three months before converting.

Rambam (22): One who was Mezanah need not wait, for she is careful not to become pregnant. The same applies to a woman who was raped or enticed.

Poskim

Shulchan Aruch (EH 13:5): A convert or freed slave must wait 90 days if she was married beforehand. Even if her husband converted with her they must wait, to distinguish whether the child was conceived before or after conversion.

Beis Shmuel (7): The Beis Yosef disagreed with the Magid Mishneh and said that a convert must wait in any case. He retracted here and requires waiting only if she was married, like the Magid Mishneh.

Gra (13): We hold like R. Yosi who does not require a Yisraelis to wait after Zenus, all the more so a convert!

Shulchan Aruch (6): One who was Mezanah need not wait, for she turns over at the time of Bi'ah to avoid pregnancy. The same applies to a woman who was raped or enticed or captured, even if she is an adult.

Beis Yosef (DH Kosav ha'Rivash): If a woman transgressed and had Zenus within the 90 days, she is punished only for Zenus. She need not wait longer due to the Zenus.

Darchei Moshe (3*): There is no decree of Havchanah due to Zenus.

Beis Shmuel (9): The Tur requires a captive to wait. He says that the Ramah exempts. The Beis Yosef says that this is like R. Yosi. This is wrong. The Tur does not bring the opinion of the Rif and Rambam that the Halachah follows R. Yosi. Rather, he is lenient because there was not a Vadai Bi'ah, but a convert almost certainly was Mezanah.

Rema: Some say that all of these must wait if they are adults who can become pregnant. If a married woman was raped and she did not have relations with her husband beforehand, she must wait.

Source (Darchei Moshe citing Or Zaru'a): If she had relations with her husband beforehand she need not wait, for we attribute the child to him.

Chelkas Mechokek (5): It depends on whether or not she had Bi'ah with her husband in the last three months. According to those who rule like R. Yosi in any case she need not wait.

Levush: If she had Bi'ah with her husband she need not wait, for it would not help, for in any case perhaps she is pregnant from her husband.

Teshuvas Ha'Elef Lecha Shlomo (EH 70): The Rema connotes that it does not matter when the Bi'ah was. Since if she had Bi'ah with her husband in the last three months she need not wait, we do not distinguish and exempt her whenever she had Bi'ah with him beforehand. In mid'Rabanan laws we sometimes say 'Lo Plug' to be lenient. In particular we can be lenient about Zenus and rape because some exempt, even though we normally are stringent. However, from the Darchei Moshe it is clear that we are lenient only when we can attribute the child to her husband, i.e. they had Bi'ah in the last three months. If her only Bi'ah with her husband was her first, it could not make her pregnant, so she must wait.

Note: We should similarly say that if she never had Bi'ah before she was raped no Havchanah is needed! Presumably, the Or Zaru'a relies on the majority (most Bi'os are with her husband - Sotah 27a) and/or assumes that she turned over after she was raped. The Rema did not mention three months. It is logical to exempt only if she had relations shortly before she was raped (both according to the Or Zaru'a, and the Levush). If her last Bi'ah with her husband was two months before the rape, we should require Havchanah in case she will give birth eight or nine months after the rape. This is surely not from before the rape, but if she will not observe Havchanah we will have a Safek; perhaps it is from her husband after the rape!