Lovely post!

One of the thing about most science or the scientific theories you describe is that they are often approximations.
It doesn't mean they're incorrect, but they might be correct only in certain instances or to a certain degree of accuracy. An easy example is how we view movement and speed. If you're travelling at a small speed compared to the speed of light, adding 2 movements together is very easy and does seem to give the right answer. However, if you consider special relativity, you'll see that the calculations get quite a lot more complicated. And you'll also see that the answer is almost the same at low speeds, yet drastically different at speeds close to that of light.
This doesn't mean that the classical way is wrong, it's just only correct at small speeds.
And that's just one simple example. There are just so many places where something like this is used, most models nowadays are linear while a lot of the processes themselves are nonlinear for example.