some achronim write that when the rishonim seem to argue with chazal on medrash, what they’re doing is saying that “lulei hakabalh” we could have said this or that, or that there’s a level of pshat, within pardes (pshat remez drush sod) which can fit this meaning, even thouygh it’s not in chazal – evidence of this can be found in, for example, the ibn ezra’s statements that “kol divreiheim emes” when referring to chazal.
you won’t find achronim arguing with chazal or not accepting midrashim; that needs to be stated.
That is, until maskilim came and decided that medrash doesnt fit their worldview and that they’d rather think that the avos and shvatim were ordinary people who happened to be aware of Hashem.