The scientific method is based on a flawed axiom that we can know the reality through our senses. Unfortunately all human beings are subject to four defects:
1) Our senses are limited and imperfect
2) We make mistakes
3) We are in illusion
4) We cheat.
Due these defects we can not know the Truth through this method. In order to have perfect knowledge you must hear from higher authority. Just like if you want to know your father you have to ask your mother. You can't go to every man and test them.
Science does a way better job of explaining the universe than religion or higher authority does. And being in a physical reality, all we have to rely on is our senses and ways to measure the authenticity of what we observe through testing.
1.) Our senses are limited and imperfect- that's why we make machinery that can expand those senses. There are robots that can smell and detect any trace of a scent, right down to the chemical level. There are telescopes bigger than my house to see into the universe. Hell, there are even 3D printers now that can create material. We can make almost every kind of machine or invention to further our senses in understanding the universe.
2.) Yes, humans make mistakes. That's why there is trial and error. That's what makes science an ever-evolving and expanding field. Once we figure out something is wrong, we figure out a way to fix it. It's always changing according to new discoveries about the world.
3.) I don't quite get what you mean by we are in illusion. Illusion of what?? Please verify.
4.) Yes, humans cheat. But the scientific community at large has policies and ways to check for cheating. You don't think they let someone publish an article that completely fabricates findings without letting other peers review their work for authenticity and verification?? If you can't reproduce the same results of an experiment, then that experiment is false. If it is true, then scientists can use the same exact methods to produce similar or exact results.
Nobody can achieve perfect knowledge. Knowledge is changing all the time. All we can do is look at the facts of the universe that we already know and keep looking for more answers to questions that we postulate.