Probability in science is used to quantify our ignorance. Our ignorance of the way the universe works can be minimized, but never fully eliminated.

Science is an inductive process, meaning that it accumulates evidence and observations, and then distills them into models that we can test through further experimentation. This approach can never create absolute "truth" because models are only as good as the data used to build them. Since we can only ever accumulate a finite amount of evidence in a limited number of situations, we can only become more confident in our models' predictions. To be certain of the result of an experiment, we would need to have validated our model in every possible situation with an infinite number of trials (impossible), and be fully aware the entire state of the universe at the moment of the experiment (also impossible).

There are some things that are simply beyond our ability to know. The nature of the universe may drastically change at any moment, due to possible events outside of our universe. Any number of global extinction events may be rushing toward the Earth at the speed of light, such as a gamma ray burst, false vacuum collapse, or something we can't even comprehend at the moment. We wouldn't even be able to observe them until the very instant we, along with the apple and possibly the Earth itself, are all destroyed.

The fact that we cannot be fully certain that a dropped apple will fall to the ground is irrelevant to our daily lives. Your girlfriend has a much, much higher chance of dying in a car crash on her way to work than gravity failing. It's just scientists being pedantic about the way the inductive process of science work in reality.

"Essentially, all models are wrong