This is a common mistake that everyone does while jumping to google tag manager from google analytics. If you have decided to use google tag manager and setup google analytics using tag manager, you have to be careful.
Before installing google tag manager on your site make sure to remove the analytics tracking code from all the pages. After removing analytics tracking code, setup google tag manager and insert the tag manager container code on your site.
Next create a new tag to setup google analytics using tag manager. Installing Google Tag Manager on wordpress is an easy tutorial for setting up tag manager in WordPress and link analytics account. But if you are not using WordPress, to connect google analytics with tag manager read from “How to connect Tag Manager to Google analytics” section.
Once you setup GTM properly on your site you will not further see mismatching and discrepancies in your reports.
See the original question here: https://productforums.google.com/forum/#!topic/tag-manager/gHnrg3lLM9Q;context-place=forum/tag-manager