Our Gemara on amud beis discusses the procedure of tithing animals.  Animals born from this year's cycle are put in a corral, and one by one, pass through a gate, counted by a staff.  Every tenth sheep is tagged with a red mark and becomes masser (Mishna Bechoros 9:7).  If a counted sheep somehow jumps over the gate and returns back to the non-tithed group, the entire group is now rendered exempt from any further tithing procedures.  The Biblical directive is to count with certainty, and since there is one exempt sheep mixed within this group, the count is no longer certain.

Tosafos here raises the question as to why do we not say that the already tithed sheep becomes subsumed and nullified, as there is a general Torah principle of following the majority.  Tosafos says we cannot answer that with the additional principle that if an item has enough distinctiveness that it is counted and sold individually instead of by volume, it is not subsumed under a majority. (Davar Shebiminyan, afilu b’eleph lo batel, see Shulchan Aruch YD 110:1.) While this principle is true, Tosafos says it is a rabbinic enactment and thus could not be used to exempt a Torah obligation to tithe, as the animal should be subsumed under the majority and considered un-tithed from the strict Biblical perspective. 

Sefer Daf all Daf quotes a Chiddushei Harim that offers a clever answer, and an interesting metaphysical idea taken from it.  Chiddushei Harim says that the rabbinic idea that an item which is counted individually is not batel comes from a Biblical concept, and as with many rabbinic enactments, they are based on an existing Torah principle (K’eyn Doraysa Takun, Pesachim 116b.) Thus, there can be something that is so distinct, even from a Biblical perspective it is not subsumed. Since the Torah itself mandates that the animal be counted, it makes it into a “Mega” DavarShebeminyan. Based on this, Pardes Yosef (Mishpatim) explains that this can be used as a retort to the gentile who disputed the rabbis (Vayikra Rabbah 6:4) by arguing, “Your own Torah states to follow the majority (Shemos 23:2). If so, why do you people not follow the consensus of the other nations and worship other Gods?  Pardes Yosef says since the Jews are counted in the Torah, they are given a distinctiveness and valuation that is not subsumed under the majority,

The actual verse that discusses the mitzvah to count the Jews, presents an interesting formulation and apotropaic prescription. It states in Shemos (30:12):

כִּ֣י תִשָּׂ֞א אֶת־רֹ֥אשׁ בְּנֵֽי־יִשְׂרָאֵל֮ לִפְקֻדֵיהֶם֒ וְנָ֨תְנ֜וּ אִ֣ישׁ כֹּ֧פֶר נַפְשׁ֛וֹ לה׳ בִּפְקֹ֣ד אֹתָ֑ם וְלֹא־יִהְיֶ֥ה בָהֶ֛ם נֶ֖גֶף בִּפְקֹ֥ד אֹתָֽם

When you take a census of the Israelite men according to their assignments, each shall make a payment of requital to Hashem, so that no plague may come upon them through their being enrolled.

What aspect of counting requires an advance donation in order to ward off a plague?  Rashi explains that the counting arouses the evil eye, and thus to ward off those effects, a special donation is required. Rabbenu Bechaye and Malbim (ibid) explains that being counted invites additional scrutiny, and brings about judgment as an individual instead of as part of a whole nation. An outcome of this thinking is that making efforts in your heart to join with the rest of the Jewish people serves as a protective measure. The sentiment and behaviors of one heart and one people, lead to a shared group merit. 

The Mareh Yechezkel (Parashas, Ki Tisah and Parah 5) adds a derash to underscore this point: The phrase used by the Torah for the payment is described as “Kofer Nefesh”, which has the same root (K-F-R) denial. Thus, the Torah is hinting that one might become too proud of his accomplishments, worship his own ability and deny God’s providence. Thus when we stand out and are counted, or when we are counting our own achievements, we must be careful to atone for our denials of God’s providence mixed within our pride.