Ideally, there never should be an instance of Halakha versus common sense. As we shall soon see, while the Torah may not always be provable through deductive reasoning alone, it should never ask us to believe something that is patently unreasonable. I feel compelled to a write this in response to fundamentalist trends that seem to make virtue out of blind acceptance. Granted there is a certain logic to such a position, perhaps considering that G-d may be testing us. While some may believe this to be so, Maimonides in his Guide for the Perplexed  (III:25) unequivocally and categorically rejects this notion. (Despite certain verses that appear to be in contradiction to this. He goes into detail suggesting various refinement in interpretation that is beyond the scope of this article.)

Furthermore, I submit two sources two indicate that Halakha should not, in principle, trump the well-being of those who adhere to its beliefs and practices.  This is, of course, aside from common sense if a particular halakhic practice actually presents serious consistent danger based on known circumstances and chazakas.):
1. The Talmud (Succah 32a) clearly uses the principle that the Torah’s ways are pleasant in order to rule out a particular choice of branch that would have been plausible as the scriptural intent for one of the four species. The exclusionary reasoning was not exegetical but rather because the plant under consideration had thorns and this would be hurtful to hold in one’s hands. Ergo, the Torah could NOT POSSIBLY have intended that particular plant to be used as part of The mitzvah.
2. Rav Saadiah Gaon In Emunot Vedeot, (Treatise 3, chapter 8) states explicitly that no prophet, even Moses, and even by force of miracles and wonders had the power to represent their statements as the word of God if they run counter to human reason . That is, we would not be expected to believe him. Here is the quote :
“The basis of our belief in the mission of Moses is not solely the miracles and marvels that he performed. The reason for our believing in him, and in every other prophet, is rather the fact that he first called upon us to do what is proper. Then, when we had heard his appeal and saw it was proper, we demanded from him miracles in support of it and, when he performed them, we believed in him. If, however, we had felt that the appeal he made at the beginning was not proper, we would not have demanded any miracles from him, because miracles are of no account in supporting the unacceptable....hereon the same procedure is to be followed in the case of every claimant of prophecy. If he says to us, “My Lord commands you to fast today,” we ask him for a sign in support of his mission, and when he shows it to us, we accept it and fast. If, however, he were to say to us, “My Lord commands you to commit adultery and steal,” or “He informs you that He is about to bring a flood of water upon the world,” or “He makes it known to you that He created heaven and earth thoughtlessly while He was asleep,” we would not ask him for any sign, since what he called upon us to do is not sanctioned by either reason or tradition. Now I have seen one of the proponents of the theory that has just been discussed go further in the matter and say, “But suppose we note that the [pretended] prophet pays no attention to us but makes us witness the miracles and marvels so that we see them perforce. What shall we say to him in that case?” My answer was that our reply to him should be the same as that of all of us would be to anyone who would show us miracles and marvels for the purpose of making us give up such rational convictions as that the truth is good and lying reprehensible and the like. He was thereupon compelled to take refuge in the theory that the disapproval of lying and the approval of the truth were not prompted by reason but were the result of the commandments and prohibitions of Scripture, and the same was true for the rejection of murder, adultery, and stealing. When he had come to that, however, I felt that I needed no longer concern myself with him and that I had my fill of discussion with him.“
Now of course, I am not suggesting Halakhic anarchy, whereby persons reject Halakha merely because it does not make sense to their thinking. After all, we are all fallible to our own biases and needs that can distort logic. However, this is proof of concept and particularly relevant to the reasoning process of a posek (halakhic decisor). Specifically, this suggests that if a posek, through his sound and sincere reasoning concludes a ruling that appears counter to reasonability or common sense it at least calls for that he pause to consider that he is in error, though not everything that appears to be unreasonable is always so.
One final point, while Maimonides and Rav Saadiah Gaon maintain that the Torah ought be reasonable, this is on a large scale basis. It is quite possible that a precept in the Torah, which is generally beneficial, may be harmful to an individual. (This does not abrogate the covenantal responsibility to adhere to the commandment, but it does offer some mitigating factors that could reduce but not eliminate culpability.) Maimonides states in his Guide for the Perplexed (III:34):

It is also important to note that the Law does not take into account exceptional circumstances; it is not based on conditions which rarely occur. Whatever the Law teaches, whether it be of an intellectual, a moral, or a practical character, is founded on that which is the rule and not on that which is the exception: it ignores the injury that might be caused to a single person through a certain maxim or a certain divine precept. For the Law is a divine institution, and [in order to understand its operation] we must consider how in Nature the various forces produce benefits which are general, but in some solitary cases they cause also injury. This is clear from what has been said by ourselves as well as by others. We must consequently not be surprised when we find that the object of the Law does not fully appear in every individual; there must naturally be people who are not perfected by the instruction of the Law, just as there are beings which do not receive from the specific forms in Nature all that they require.”