SecularFrummy,
I think your original OP question belies a false dilemma fallacy. You are attempting to force a choice between two options: either the Rishonim were infallible (i.e., superhuman or deity) or we must find a means to determine their errors, and question their rulings. This is fundamentally not logical.
When I was in high school, I once solved a long mathematical problem and came up with a different solution than the textbook’s. I brought the problem to the teacher, who took a look and realized that there was an error in the textbook. I was praised for my work and for not being satisfied with blindly accepting the textbook’s solution as correct by default.
Looking back, I think that ultimately this incident had a more negative effect on my future learning than a positive one. For a long time afterwards, if I solved a problem and arrived at a different answer from the textbook or the teacher, I would be more inclined to stick to my guns and argue that my solution was correct. After all, textbooks are not perfect and can have errors! It turns out that errors in high school math textbooks are exceedingly rare, and errors in high school student math homework are common.
Rather than coming up with my own solution, and dismissing the textbook’s solution as wrong and ending my thoughts there, I would have been much better served by digging deeper into what I viewed as the wrong solution, working backwards and discovering my own mistakes.
Yes, the acharonim, rishonim, tannaim, amoraim, the sages of the Sanhedrin, the prophets, judges, and our forefathers were all human beings. Human beings are not infallible and can make mistakes. It is much more likely, however, for me to make a mistake in my Torah learning than our sages, so ultimately it is much more productive to look for my own mistakes than it is to look for theirs if the answers don’t line up.
It is also most likely that if there was a mistake, it has already been addressed by another sage.