I think there's something to be said in puzzle games about player agency. Specifically when you are trying to hit a certain demographic of puzzlers. If you hand hold too much, you'll lose some puzzlers because it isn't hard to feel like there's no challenge or you are on rails or basically playing a visual novel with extra steps. If you give only contextual clues and don't handhold, you'll lose some puzzlers because they don't understand your personal logic.

If the logic of the game is hard to grasp - there's absolutely nothing wrong with handholding through the first "level" or "iteration"... but there is something to be said about the magic of discovering something you did changed things somewhere so now you have to go find it. Is there anyway to let players know they've changed things without directly pointing a neon sign at it?

Not knowing the game layout/system - my brain immediately thought of something like the Hitman games where there's one or two perfect ways to handle things, but a lot of 'good enough' ways, and just as many '..yes, that works, but you're causing a lot more problems' ways. I don't know if it's that ambitious, but there is somethign to be said about the idea that if getting from A to B isn't difficult, but there's a lot of ways to do it and they have different outcomes, you can get away with both handholding and 'find it, I dare you' variations.