The rabbis in the midrash saw a connection between the end of parshas Shlach (where the mitzvah of tzitzis appears) and the beginning of parshas Korach (which describes the rebellion against the authority of Moseh Rabbeinu). Korach claimed that since all Jews have the same level of kedusha, everyone has the right to interpret the halacha as he sees fit. His argument against Moshe's halachic position had great appeal to the masses. It was based on common sense. Korach got two hundred and fifty Jewish leaders to wear four-cornered garments made of techeiles and to appear before Moshe, asking whether it was necessary to tie the techeiles strings (in tzitzis) to their garments. Common sense dictated that this was not necessary. If one string dyed techeiles takes care of a garment of any other color, then if the entire garment consists of techeiles strings, no additional strings of techeiles ought to be needed.
Moshe Rabbeinu, on the other hand, argued that halacha is a self-contained discipline where common sense does not always play a role. In the discipline of biology the Talmud points out that one can not always use common sense; and the same is true of physics. Each discipline is self contained, and has its own style of logic. The same is true of the halacha.
This idea is well known at Yeshiva. Rav Soloveitchik's talk on this topic has appeared both in Shiurei Horav (edited by Joseph Epstein) as well as in Reflections of the Rav, volume I (transcribed by Rabbi Avraham Besdin).
In connection with this idea many will refer to the words of the Sema (in his commentary to Choshen Mishpat) that the "sechel of the baal habayis" is just the opposite from the "sechel of the Torah" (in yeshiva parlance a "baalebatishe svora" usually refers to a common-sense argument.) In yeshiva circles a witty comment is attributed to the Ohr Sameach: when a talmid chacham can not figure out any given halacha, let him ask a baal habayis, and then do the opposite. The halacha will always be the opposite from what the baal habayis will think that it should be. The story goes that on one occasion the talmedei chachamim did not know what the halacha should be in a certain instance, they asked a baal habayis, and he happened to give the right answer. They approached the Ohr Sameach and asked him, but didn't you tell us that the sechel of the baalei battim will always be the opposite from the sechel of the Torah? Whereupon he answered that the baal habayis must have had a bad day! He was not thinking straight for a baal habayis!
I remember there was a student in Rav Soloveitchik's class at Yeshiva who would evaluate the shiurim. When everything made sense, there were no loose ends, and everything fit into place, that would be considered so-so. But when the svoros developed were not that compelling, and all the gemoras didn't really fit in well, that was tops - "real Brisk"!
In fact, in Lithuanian yeshivas there was such an exaggerated disdain for baalei batim, the "story" went around about two elderly gentlemen - baalei batim of course - who were both hard of hearing and made up to learn gemorrah together. One was using a gemorrah Eruvin while the other was using an Erchin. The chavrusa went very well, until they reached the forty-third daf, when one was already making a siyum on the smaller volume (Erchin), and the other still had another seventy blat to go!
This exaggerated attitude is the basis of the very fundamental philosophical question that bothered many of the Lithuanian yeshiva bochurim: why did the Borei Olam create baalei batim at all? We know that he didn't create anything that has no purpose!?
Needless to say, all of these exaggerations are ridiculous. The Sema never meant to say that the sechel of baalei batim is always the opposite from sechel haTorah. A layman who is not familiar with the intricacies of physics or biology will often be mistaken if he will apply common sense to those disciplines; and the same is true of the self-contained discipline of Torah. But very often we will use common sense in establishing halacha! The Talmud tells us that by way of sevorah we can establish a din de'oaraisa!
I recently met a young talmid chochom who insisted that a certain halacha in Shulchan Aruch must be understood literally, as applying in all cases, even when it made no sense. I argued that it was self understood that one should use his common sense, and only apply the halacha when it indeed did make sense. (I later checked the Iggros Moshe of Rav Moshe Feinstein and he wrote exactly the same in that particular instance). This young talmid chochom told me, no, we may not use common sense at all, and even though the halacha - as he misunderstood it - made no sense, he has "emunas chachomim." I told him that this was a Christian concept (the principle of the infallibility of the posek). Our Torah speaks of the theoretical possibility of a par he'elem davar shel tzibbur, a korban brought in a situation where all seventy one members of the Sanhedrin paskened wrong. The torah tells us that on one occasion Moshe Rabbeinu was about to issue an incorrect psak, until he listened to his brother Aharon and corrected his position.
In our religion, are we not permitted, or better yet - obligated, to ask questions when we come across a halacha that makes no sense? Isn't that what "lernin" is all about: to make sense out of the halacha! Our Torah is a Toras emes: it corresponds to reality, and does not contradict it! Rav Chaim Volozhener would often sign off at the close of a tshuva "Kel emes nosan lanu Toras emes, u'bilti el ho'emes eineinu - the true G-d gave us a truthful Torah and we always have to try to be honest to discover the true meaning of the halacha." If there are two ways to understand a halacha, one which makes sense and the other does not, of course we should choose the interpretation that makes sense!
Yes, indeed, emunas chachomim is a very fundamental principle in our faith: we believe Hakadosh Baruch Hu will give divine assistance to an honest and deserving talmid chochom that he should be above his personal negios in issuing a psak; he will not have an agenda. But it doesn't mean that we should believe in nonsense. Every exaggeration is by definition not true. It does not correspond to reality. The halacha is very nuanced because the world is very complex. Most simanim in Shulchan Aruch have many se'ifim. You can not cover all the cases in one short statement. The challenge of "lernin" is to be able to formulate the halacha precisely, without any exaggeration leaning in either direction, with "sechel". [1]
[1] See Did the Rabbi Distort the Psak?, Why Was the Torah Forced Upon Us?, and All Men Are Created Equal, for further discussion regarding Emmunas chachomim