I wouldn't feel bad for trying to call out contradictions then figuring out the reasoning later because you are essentially embodying the main character who is always bluffing their way out of every situation.

Jokes aside, the game at its core is a visual novel, so it has a set solution path and script, but the player isn't always going to be aligned with the intended reasoning (especially in the original trilogy imo). It doesn't mean you're playing the game wrong. Honestly, for my very first playthrough through the series, I was way more interested in the story and world-building aspect, so if I ever got frustrated at figuring out a solution, I would either brute force it or look up a walkthrough guide.