The Rambam (Shemoneh Perakim, end of Chapter 6) deals with different types of mitzvos. He says one type are logical, and thus a perfected person shouldn't want to transgress them. He says some call these mitzvos sichliyos, logical mitzvos. He lists murder, theft, robbery, overcharging, and damaging others as examples. The Rambam writes that these are mitzvos that Chazal describe as שאילו לא נכתבו ראוים הם ליכתב, if they weren't written in the Torah (as prohibitions), they would have deserved to have been written. Meaning, they would have been forbidden because of logic.
He then describes mitzvos that are beyond human logic. These mitzvos a perfected person can desire to transgress, yet won't because G-d dictated not to. If the Torah hadn't forbidden them, they wouldn't have been considered evil. These are commonly referred to as chukim. He lists milk and meat, shaatnez, and forbidden relations as examples of this latter type.
My edition of Shemoneh Perakim has a note (from הגהות בד"ו, my guess is that stands for a marginal note in the sixth printing) that the Rambam's source for his first category is Yoma 67b. It points out that we find a contradiction there to the Rambam's words. There, the gemarra teaches:
ת"ר (ויקרא יח, ד) את משפטי תעשו דברים שאלמלא (לא) נכתבו דין הוא שיכתבו ואלו הן עבודת כוכבים וגלוי עריות ושפיכות דמים וגזל וברכת השם
The Sages taught with regard to the verse: “You shall do My ordinances, and you shall keep My statutes to follow them, I am the Lord your God” (Leviticus 18:4), that the phrase: My ordinances, is a reference to matters that, even had they not been written, it would have been logical that they be written. They are the prohibitions against idol worship, prohibited sexual relations, bloodshed, theft, and blessing God, a euphemism for cursing the Name of God.
We see that the Rambam's source for logical mitzvos includes forbidden relations, but he included those in his list of mitzvos that are beyond human reasoning. This is a glaring contradiction.
The note suggests a partial answer from the Maharsha there. He understands the gemarra differently than I explained above. The gemarra doesn't mean that if they weren't written, they would have been self evident. Rather, it means if they hadn't been written, they would have been forbidden anyways, since they are forbidden to benei Noach. The Rambam could mean that even before forbidden relations were forbidden to benei Noach, they would have been considered permitted. The problem is, seemingly the Rambam's source for his first category of mitzvos is this very gemarra, and he doesn't seem to be understanding it like the Maharsha.
Edit: I just saw that in Rav Kafih's edition of the Rambam's commentary on Avos (fn. 14) that he writes it is clear that the Rambam didn't have the words גילוי עריות in his gemarra. Haven't checked if there are any manuscripts that confirm his suggestion.
Are there any other resolutions to this contradiction?