Traditional commentaries generally don't deal with trying to make an argument sound logical, but rather with settling contradictions (of statements or of logic). If you are new to Gemara then the logic can be at odds with your way of thinking. But it is taken for granted that it is indeed logical. If your efforts are spent on making sense of it, rather than judging it, you will eventually be able to neatly wrap your brain around the Gemara's logic.
There are a few types of answers that might require a general introduction. For example, reading words into a Braysa or splitting statements into multiple opinions. But I doubt that you have come across this problem very often, and this wouldn't be a bad place to bring them up when you do.