How to deal with grammatically incorrect suggestions from my advisor on master's thesis? I'm writing my thesis in English. English is neither my or my advisor's mother tongue. I'm now doing some corrections that were suggested. Some of them refer to the content of my  thesis and some of them refer to the language.

How should I deal with the suggestions that are obviously wrong? For example suggesting I put a comma before if or use a future tense after once. I don't want to intentionally make any grammatical errors in my thesis. 

I agree with most of what is pointed out. There are only few amendments that I take issue with. 

Should I just ignore his wrong suggestions? But then he may notice that I haven't changed what I was supposed to when he reads my thesis again. 

Should I explain to him why I haven't changed what he suggested? I could quote some websites (when I disagree with what he proposes, I always look it up). Wouldn't that be rude?
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.