1. When submitting your work, tell the reviewer what you want your story to be
It is the job of the reviewer to provide feedback that helps you make the story what you want it to be.
And, while not every story requires explanation, if you have specific goals, or concerns, or (better yet) a model story, similar in style, this can only help the reader understand where you want to take things.
Also, if there are ‘rules’ for the story, you should reveal them. For instance, ‘no real magic’ is a rule for my current novel, a book that contains magical elements that are later revealed to be either well founded in fact, or total lies. Other ‘rules’ may be important in a given genre, but unfamiliar to readers of other genres, or may be rules of the genre the author purposefully intends to break.
2. Expect a variety of responses, some contradictory, and focus on what most people feel is a problem
Feedback can be good or bad, helpful or not, and can either just identify a problem or also offer a proposed solution.
It is like a poll, except you know the respondents well enough to weight their responses--some count more than others.
In general, however, you want to focus on those aspects of the story that most people identify as problematic, even if some of the comments define the problems differently, or contradict one another. Something is wrong here. That is the message.
How to fix the problems is a separate matter. Proposed edits at a paragraph level are usually easy enough to adopt, adapt, or reject.. Larger issues though require more thought, and it is often best to put the most difficult issues on the back burner while quietly working on something else.
In any case, whatever you do, don't go bland and paint over everything in beige. Often, the fact that something does not work means you were not brave enough to go take it far enough. So, be brave, and try harder to get to the heart of things. There needs to be real emotion in what you write. Stripping it out in response to comments is always a mistake.
Sometimes too, a complaint can be something your character can directly confront as a part of the story itself. For example, if your heroine seems not to fit the reader's idea of who such a person should be, you can make this something she must deal with as part of the story itself--"she never fit in with her family's expectations, her mother had wanted a girly girl, and her father had not wanted a girl at all."
You are the custodian of your story--it's protector. And it is no crime to ignore comments you feel are off the mark. Or to ignore comments for the moment, and revisit them in some later revision cycle. This is especially true for longer work, where it may be best to accumulate feedback over a number of chapters, or an entire section or more, before acting on it.
3. Depend on people’s first pass feedback to identify what is confusing or otherwise off the mark
Because you have the story in your head, in full, it is easy to fail to explain details that later baffle readers.
Is your protagonist young or old? Male or female? What are they thinking? Or feeling? And so on.
In particular, unless there is good reason to withhold details, it is best to provide enough information for the reader to 'see' and emotionally experience (with all the senses) what you describe.
4. Learn to slough off reviewers’ bad behavior and outrageous remarks by sharing your own worst experiences with others
Everyone, even the best of writers, has had to deal with bad reviews and stupid remarks. There are even collections of bad reviews for works later regarded as great or classic (Shakespeare got bad reviews on many of his most notable plays, and Nabokov could not get Lolita published except by a publisher who specialized in pornography, etc., etc.).
Even better though, are off-the-mark remarks taken from your own experience. Swap a few ‘war stories’ with fellow writers, laugh at a few of crazy things people have said in workshops or in written critiques, and you’ll lose all respect for reviews and reviewers--a generally healthy attitude, and one that helps you more easily ‘ignore those comments you strongly disagree with.’ At least until you, years later, finally understand what that misunderstood comment was all about. It cuts both ways.