Daily Mitzvah (Rambam)

Do not count a preparatory act as an independent mitzvah.

E.g., "You shall take fine flour and bake it [into] twelve loaves" (Leviticus 24:5). This is not an independent mitzvah, but a necessary prerequisite to the mitzvah of placing Showbreads on the Table in the Temple's sanctuary. Similarly, "Command the children of Israel, and they shall take to you pure olive oil" (Exodus 27:20, Leviticus 24:2) is not counted as one of the 613 mitzvot, rather it is a preamble to the mitzvah of kindling the Temple Menorah daily.

If a mitzvah is comprised of a number of elements, do not count them separately.

E.g., "And you shall take for yourselves on the first day [of Sukkot], the fruit of a beautiful tree, date palm fronds, a branch of a braided tree, and willows of the brook" (ibid. 23:40). All these individual elements come together to create a single mitzvah—the mitzvah of taking the Four Species. As such, they are collectively counted as only one mitzvah.

When commanded to do a certain action, do not count each part of the action separately.

E.g., "They shall make Me a sanctuary" (Exodus 25:8). There's a general mitzvah to construct a sanctuary for G‑d. For this purpose, it is necessary to construct an Ark, a Menorah, altars, etc.,—but these are all details of the overarching mitzvah of creating a sanctuary for G‑d.

We do not count the amount of days a mitzvah is performed.

E.g., we are commanded to dwell in a sukkah during the seven days of the holiday of Sukkot—yet this is one mitzvah. We are commanded to bring a special offering in the Temple on Rosh Chodesh—yet this is one mitzvah, not twelve. We are commanded to make pilgrimage to the Temple thrice yearly—but this is one mitzvah, the mitzvah of pilgrimage.

We do not count the punishment administered for each transgression.

The Torah specifies many forms of punishments that the courts administer: Four types of capital punishment, corporal punishment, financial remuneration, sacrificial penalties, etc.,

While each form of punishment constitutes an independent mitzvah, we do not count the penalty for a particular transgression as part of the 613. For example, there are many different transgressions that mandate the bringing of a sin-offering. Yet, the bringing of a sin-offering is counted as only one mitzvah.