1) THE NUMBER OF MITZVOS IN THE TORAH
QUESTION: Rebbi Akiva and Rebbi Yishmael disagree about the status of three acts, whether they are voluntary (and not Mitzvos) or whether they are obligatory (and are Mitzvos). Rebbi Yishmael maintains that the Kinuy of a woman suspected of adultery, a Kohen's act of becoming Tamei in order to bury his close relatives, and the injunction against freeing an Eved Kena'ani are all voluntary acts. Rebbi Akiva maintains that they are obligatory.
TOSFOS here (see also RAMBAN, end of Shoresh Rishon, Sefer ha'Mitzvos) asks how can the Tana'im disagree about whether or not these acts are Mitzvos. The Gemara and Midrash state in many places that there are 613 ("Taryag") Mitzvos. The Tana'im should simply count the other Mitzvos in the Torah and, based on the outcome of that count, determine whether these three acts are included in the 613 Mitzvos.
ANSWER: The MAHARSHAM quotes the SEFER MA'AYAN HA'CHOCHMAH who explains that Rebbi Yishmael -- who maintains that these three Mitzvos are voluntary -- follows his own reasoning expressed elsewhere. The Mishnah in Menachos (28a) states that the four Tzitziyos on the four corners of a garment are "Me'akev" -- they are all part of a single Mitzvah, and if one is missing the Mitzvah of Tzitzis is not fulfilled. Rebbi Yishmael there disagrees and says that the four Tzitziyos are considered four separate Mitzvos and are not "Me'akev" each other. (The Gemara explains that according to Rebbi Yishmael, when a person wears Tzitzis on only three corners of his garment, each one is considered the fulfillment of a Mitzvah, and if he walks into Reshus ha'Rabim wearing the garment on Shabbos he does not transgress the Isur of Hotza'ah. According to the Tana Kama, he is liable for Hotza'ah because he does not fulfill any Mitzvah until all four Tzitziyos are on the garment.) Since Rebbi Yishmael maintains that there are three additional Mitzvos in the Torah (since each Tzitzis is an independent Mitzvah), he maintains that these three Mitzvos -- Kinuy, Tum'ah, and freeing one's Eved -- are not included in the count of Mitzvos but are voluntary.
Rebbi Akiva, who maintains that these three Mitzvos are obligatory and are included in the count of 613, follows the view of the Tana Kama in Menachos there, that all of the Tzitzis are "Me'akev" the Mitzvah, and one fulfills the Mitzvah only when he has four Tzitziyos on the four corners of his garment.