There are many disagreements about how Science should be done, what methods used, its purpose, what conclusions we can
draw, what conclusions we should
draw, whether we can ever be certain of something, what its limits are or should be, how and to what extent it interacts and informs other areas of thought/investigation, how open the theory and processes are to modification, etc.
wiki gives an overview:http://en.wikipedia.org/wiki/Philosophy_of_science
a book suggested by a college science professor who used to post here:
What Is This Thing Called Science?, by Alan F. Chalmers
and I found this book to be a good companion text (as it was intended to be):
Science And Its Fabrication, by Alan Chalmers