I assume you're talking about things like level 3? I mean, the run button is there. I guess we could remove the run button if it makes certain puzzle solutions feel too speedrun hack-y?
I understand what you're saying, and especially for these early levels there should be designs where you don't need to use the run button to complete the puzzle - but then, later levels that require the run button will be much more confusing due to never introducing the mechanic, and at that point we should just cut the function out entirely.