Gemara

41b (Beraisa): (An Olah must be a) "Zachar", and not a female.

Another verse requires Olah to be "Zachar". It excludes Tumtum and Androginus.

This is unlike the first Tana of our Mishnah. He is unsure about the gender of Androginus. A verse would not teach about such a Safek!

42a (Beraisa): "Ha'Zachar" excludes Tumtum and Androginus (from Erchin).

(Rav Chisda): We must delete "Tumtum" from the text of the Beraisa.

Bava Metzi'a 6b: A Safek does not enter the pen for Ma'aser. The Torah requires a definite "Asiri (tenth)".

Kidushin 73a (Mishnah): Mid'Oraisa, a Shetuki (one who recognizes his mother but not his father) is Kosher. It says "Lo Yavo Mamzer (bi'Khal Hash-m)." A definite Mamzer is forbidden, but a Safek Mamzer is permitted. A Mamzer may not marry a Vadai member of Kehal Hash-m (one of Kosher lineage), but he may marry a Safek.

Rishonim

Rambam (Hilchos Isurei Bi'ah 15:29): Why isn't a Shtuki (one whose father is unknown) or Asufi (one whose parents are unknown) forbidden to every woman, lest she is Ervah to him (e.g. his sister)? The Torah says "Al Techalel Es Bitcha Lehaznosah." Chachamim explain that if one will do so (allow his daughter to have extramarital relations, for no one will know who is the father, and), a father will marry his daughter and a brother will marry his sister. If the Halachah were that a Shtuki is forbidden to every woman, lest she is Ervah to him, such incest would not result! This teaches that we do not forbid Safek Arayos, unless she is Vadai Ervah. IF you would not say so, all orphans who did not know their parents would be forbidden to marry, lest they marry Ervah.

Rambam (18:17): The Isur of every Safek is mid'Rabanan.

Rashba (Kidushin 73a DH Mamzer): In a Teshuvah, the Rambam learned from Safek Mamzer that 'we are stringent about a Safek mid'Oraisa' is only mid'Rabanan.

Rambam (Hilchos Kil'ayim 10:27): If a thread of linen was lost in a wool garment, or vice-versa, one dyes it. Wool and linen do not absorb dye equally, so the thread will be evident, and one can remove it. If it is not evident, it is permitted. Perhaps the thread fell, for one checked and did not find it. I already explained that the Isur of Sefekos is only mid'Rabanan. Therefore, Chachamim were lenient about the Safek.

Ra'avad: This is correct, that all Sefekos are only mid'Rabanan. However, we are stringent about every Safek Torah, and lenient about every Safek mid'Rabanan.

Tosefes Yom ha'Kipurim (74a DH Itztrich): Normally, the Torah is stringent about a Safek. Therefore, the Gemara asks when a verse teaches that one must be stringent about a Safek. Therefore, we did not ask why a verse exempts Sefekos from Ma'aser Behemah. Without a verse, we would say that the tithed animal is Batel, and we must tithe the entire mixture. Regarding a Kvi, we would have been stringent even without a verse. This answers for those who hold that the Torah is stringent about Sefekos. Since Tosfos did not answer like I said, it seems that he holds like the Rambam. Toras Chayim and the Maharit say so.

Tosefes Yom ha'Kipurim (88a DH v'Ra'isi): The Kesef Mishneh says that the Rambam admits that the Torah is stringent about a Safek Kares, for one brings an Asham Taluy for it. Bnei Shmuel and the Maharit rejected this, for the Rambam discussed 'all Sefekos, whether about Tum'ah, Arayos or Shabbos', and there is Kares for Arayos and Shabbos. I do not understand them. If the Safek were permitted, why does one bring a Korban for it?! The Ran said that it is Dochek to say that the opinions that argue about whether one brings Asham Taluy without Isur Kavu'a, they argue about whether the Torah forbids a Safek (without an Isur Kavu'a, and all forbid when the Isur was Kavu'a. The Maharit says that indeed, they argue about this! The Kesef Mishneh says that the Rambam agrees about an Isur Kares, (i.e. when the Isur was Kavu'a), for one brings an Asham Taluy for it! Bnei Shmuel and Maharit mistakenly thought that the Kesef Mishneh holds that the Rambam holds that the Torah is stringent for a Safek Kares even without Isur Kavu'a. Pnei Moshe understood that the Rambam is lenient about a Safek Lav of Arayos and Shabbos, e.g. hugging and kissing or leaving the Techum, but he is stringent about every Isur Kares. The Rambam does not connote like this, and in a Teshuvah, the Kesef Mishneh explicitly said that it depends on Isur Kavu'a. This is why the Ra'anach said that the Rambam is lenient about Safek Kidushin.

Tosefes Yom ha'Kipurim: The Maharit says that Rava asked why Chachamim forbade Safek Mamzer, for the Torah totally permitted it. If this is the source to permit every Safek Torah, also they should be permitted like Vadai! If we are unsure which of two pieces is Chelev, if one ate one he brings an Asham Taluy. If he later ate the other, he brings a Chatas! The Pri Chodosh says that the Torah permitted Safek Mamzer even when there was an Isur Kavu'a, e.g. Safek divorce. If so, he should permit all such Sefekos. This is wrong. The Rambam says 'Ein Safek Motzi miYdei Vadai' regarding Tum'ah! I explain that Rava understood why Chachamim forbade other Sefekos, i.e. lest one transgress Vadai. Here, it is unreasonable to decree to forbid a Safek Mamzer to discourage men from Bi'ah with Safek Ervah, for then their children will be forbidden to marry.

Note: We could say that they decreed against a Safek Mamzer lest one marry a Vadai Mamzer!

Tosefes Yom ha'Kipurim: Also, why does the Tana permit a Safek Mamzer to marry a Safek Mamzeres?

Chasam Sofer (EH 1:73): The Rambam and Ra'avad hold that the Torah is lenient about the Safek (of Kil'ayim lost in a garment), even though there was Vadai Isur! Even though perhaps the thread fell, the Isur was Kavu'a. This is like we say that the Isur Melachah during Bein ha'Shemashos on Motza'ei Shabbos is Kavu'a, even though perhaps Shabbos ended. This is for Lavin. The Rambam and Ra'avad argue about a Safek Kares. The Rambam is lenient about a Safek Kares if the Isur was not Kavu'a. Kuntres ha'Safek at the end of Kapos Temarim explained this. The Rambam does not learn from Safek Mamzer, which is only a Lav, rather, from "Al Techalel Es Bitcha Lehaznosah", which he discusses in Hilchos Isurei Bi'ah (15:29). It discusses a Safek Kares that is not an Isur Kavu'a, and the Torah was lenient. The early Meforshim missed this.

Mishneh l'Melech (15:11): The Torah permitted a Safek Mamzer when the Isur was never Kavu'a (fixed), e.g. we do not know from whom a woman became pregnant. However, if a Mamzeres and three other women gave birth and the babies became mixed, the Torah forbids all of them to marry a Bas Yisrael. The Rambam holds that the Torah is lenient about a Safek Isur, but when an Isur (Kares) was Kavu'a, one brings an Asham Taluy for a Safek transgression. This is why the Ran says that it was an enactment to believe a midwife (about which baby is from which mother), but (when babies did not become mixed) he did not say that an enactment was needed to believe a mother about (the father of) her child. Even those who disagree with the Rambam agree that there is a difference when the Isur was Kavu'a, for we hold that one brings Asham Taluy only in this case (e.g. he ate one of two pieces, and we know that one of them was Chelev). We can say the same about the Heter of a Safek Mamzer.

Noda bi'Yehudah (2 YD 38): Even though the Rambam gave a general rule and said that it is mid'Rabanan that we are stringent about Sefekos about Tum'ah, Ervah, Shabbos..., a Safek whether a married woman was Mezanah is called Safek Sotah, and the Torah made this Safek like Vadai (Isur).

Pri Megadim (Sifsei Da'as 110:25, Dinei Sefek-Sefeka 25 on Shach 63): Even the Rambam agrees that the Torah is stringent about Safek Tum'ah in Reshus ha'Yachid, and one is lashed for it. We learn from Sotah. Even though the Rambam says that the Torah is lenient also about Safek Tum'ah, this is in cases such as two Nezirim (we saw that one of them became Tamei). We do not learn such cases from Sotah.

Avnei Nezer (EH 18:2): I say that a Safek Mamzer is like Safek Orlah in Chutz la'Aretz. (Ploni may give Vadai Orlah to Reuven, and if it is a Safek to Reuven, he may eat it.) I learn from the Gemara, which says that a family that became mixed (with Pesulim) became mixed. Rashi says that we leave them in the status of Safek, and in the future they are Tehorim. The Poskim and Ran connotes that even one who clearly knows (that they are Pesulim) may not reveal this. How can we permit them to transgress a Torah Isur through an action? Mid'Oraisa, all of Yisrael are responsible for each other! We must say that there is no Isur for one who does not know. Rashi says that we leave them in their Safek, i.e. for the Torah permitted a Safek Mamzer. The Rishonim totally rejected the Rambam, who says that the Torah permits a Safek mid'Oraisa. Why did Rava need to say that Chachamim forbade a Safek Mamzer, for they were extra stringent about lineage? The Rambam holds that Chachamim forbade every Torah Safek!

Suggestion: The Rambam holds that the Torah taught that a Safek Mamzer is permitted, and this was the precedent from which we learn about other Sefekos. It would be improper to forbid what the Torah explicitly permitted, if not for the reason of stringency of lineage.

Rejection (Avnei Nezer): Chachamim after the Gemara do not expound through the 13 Midos. Also, the Torah also taught that Safek Kahal Yisrael (is permitted to marry Pesulim). This is Shenei Kesuvim, so we cannot learn to other places. If one does not know about the Safek, he is totally permitted. Therefore, Beis Din or anyone else need not separate him.