On Shabbat 53b:
Our Rabbis taught: It once happened that a man's wife died and left a child to be suckled, and he could not afford to pay a wet-nurse, whereupon a miracle was performed for him and his teats opened like the two teats of a woman and he suckled his son. R. Joseph observed, Come and see how great was this man, that such a miracle was performed on his account! Said Abaye to him, On the contrary: how lowly was this man, that the order of the Creation24 was changed on his account!25This contrast between Rav Yosef and his student Abaye parallels arguments elsewhere between Abaye and his teacher (either Rav Yosef or Rabba, he simply refers to him as Mar). See Chullin 105b for examples (English pulled from Point By Point Summary):
(Abaye): I used to think that we do not wash after the meal onto the ground due to the filth. My Rebbi (Rabah) taught that it is due to the evil spirit that rests on the water.
(Abaye): I used to think that the reason we do not take something from the table in front of someone who is drinking is lest he get angry. Rabah taught that it is due to the spirit of Tzarda (dazing spells).
(Abaye): I used to think that we gather crumbs for the sake of cleanliness. Rabah taught that it is to avoid poverty.
(Abaye): I used to think that the reason we do not drink froth (on top of a liquid that was poured) is because it is repulsive. Rabah taught that it is because it leads to Karsam (a nasal drip and inflammation);
(Abaye): I used to think that the reason we do not eat a vegetable straight from the bundle is because it appears gluttonous. Rabah taught that it makes one susceptible to witchcraft.
(Abaye): I used to think that the reason we do not eat a vegetable that fell on the tray is because it is repulsive. Rabah taught that it leads to mouth odor.
(Abaye): I used to think that the reason we don't sit under gutter pipes is due to the water that flows down. Rabah taught that Mazikim (Shedim, which are beings with similarities to people and to angels) frequent the area.
(Abaye): I used to think that the reason we spill water from the top of a barrel is due to chips of wood that float on top. Rabah taught that it is lest Mazikim drank from it.Many of the commonsense reasons Abaye gives are superseded by what we might term superstitious, or else, mystically-inclined reasons, provided by his teacher.
Turning back to the gemara in Shabbos, each Amora is making sweeping homiletic statements based on this incident. Indeed, the gemara continues with two additional statements.
I would say that Abaye is not trying to simply be contrary, and to contradict Rav Yosef, when Abaye says:
On the contrary: how lowly was this man, that the order of the Creation24 was changed on his account!25Rather, I think Abaye was one of the early Jewish rationalists. Look at the "rationalist" Rishonim. When they explain Divine miracles by "natural" means, it was not an effort to discount the wonder of the miracle, and to encourage disbelief. Rather, they viewed the perfection of Creation as evidence of Hashem's absolute perfection. God set the constellations on their courses, and they continue in their set paths, and perhaps have influence on human events.
אשר במאמרו ברא שחקים, וברוח פיו כל צבאם, חוק וזמן נתן להם שלא ישנו את תפקידםA change in the natural order in order for Hashem to accomplish His design implies that there was a flaw in the original act of creation, and a perfect God does not make a flaw. That is why, according to Avos, even the mouth of the pit that swallowed Datan and Aviram, and the mouth of the donkey that spoke to Bilaam, were created at twilight at the tail-end of the act of Creation.
This would lead Abaye to regard a diversion from the natural order as sub-optimal.
Meanwhile, Rav Yosef would regard the diversion from the natural order as evidence of an engaged God, who can bend nature to His Will, for He created nature.