There will always be people who disagree with you. There will always be people who can find holes in your argument. There will always be people who think you’re doing things in the wrong way.
That’s the nature of academia. Indeed, this entire industry is built on people critiquing one another’s work (think about how you do so in your own lit review, for example).
What this means is that, no matter how hard you try, there will always be things ‘wrong’ with your writing. Your literature review will always be incomplete, your theory framework will always annoy someone somewhere, your methods will no doubt be flawed, and your discussion could have been framed differently.
None of this means you’re a failure.
What’s important to remember is that perfection in this context is illusive. No matter how hard you try, someone will always find a problem.
But rather than feel defeated, see this as empowering. It means that you can stop striving for perfection and instead strive for ‘good enough’. Work in the way you think best – and ensure that way has the proper grounding in the literature – and be prepared to counter any criticisms should they come up in your supervision meetings or viva.
You may agree with the criticism you receive, if so you should admit it and incorporate that criticism into your thesis (for that too is the nature of academia). But you may not, and if you have thought out and justified your decisions within reference to the literature you can stand your ground and argue your corner.
It’s your PhD, not theirs, so don’t let them write it for you.