When I check Google Index > Content Keywords in Google Webmaster Tools, it shows lots of unimportant keywords like: to, is, are, from, in, on, we, you and etc.That's very natural these words are found more than others because it's so hard to find a sentence without one of these popular words.I'm wondering why Google is doing this? Does it make a problem for SEO? How to deal with that? 
Content keywords are unimportant in Google Webmaster Tools
seo;google;google search console;keywords
It does not indicate an SEO problem when common words appear in the content keywords list.  I have a multi-language website for which I have each language verified as a separate site.   I only see common stop words appearing in the list (is, a, the, etc) for some of the languages.Google does not intend this list as a list of keywords for which you are likely to rank in the search results.   Rather it is a hacked site prevention measure.  If you see keywords like viagra or sex appearing in the list then you will know that malware is serving those terms to Googlebot.Having words that you actually use on your site appear high in this list is never a problem.   Even when those words are not important words.