How to deal with grammatically incorrect suggestions from my advisor on master's thesis?
It will be helpful for your advisor if you give a list of changes, and where they were implemented in the text, together with your new version of your thesis. That way (s)he won't have to read your entire text again and can just foucus on those passages that have changed. That document would also be a logical place for mentioning the changes you did not implement and give the reasons why you did not do so. 

Your advisor will probably be very familiar with this way of working; this is how we respond to reviewers when we sent articles to journals. So this should not feel strange or offensive to her or him. This does not mean that (s)he will agree with you, but that is something you can talk about at the next meeting.