There are a few reasons why you might not see some backlinks:

  1. For recent backlinks, (let's say new backlinks that are less than 2 weeks old) the crawlers that we use (and which competitors use as well) won't find all links in real time, as soon as they are created. Some they find faster, and some slower. Usually they recrawl the entire web in about 30 days or more. So for recent links, you just need to wait a bit more to see them all.
  2. Monitor Backlinks shows just one backlink per domain to prevent noise. We ignore sitewide links and links that are not LIVE. (In contrast, Google Analytics also shows links that no longer exist.) Please note that we use a variety of data sources to ensure that we get a very wide coverage of referring domains, which is what matters most for you. Particularly when you are disavowing, it's not helpful to see more than one backlink per domain, since you would generally be disavowing the entire domain and not the URL. 
  3. The links are orphan pages (pages with no backlinks). Since no one links to orphan pages, it's hard for any web crawler to find it (including Google). This might especially be relevant if you are dealing with negative SEO.  
  4. The links are created dynamically using javascript instead of regular HTML. That makes it much harder for our web crawlers and also Google's crawlers to find them. This tends to be common with either social media websites or website builders (eg. Wix, Squarespace, Weebly). They have traditionally been deemphasized in SEO either (ie. they haven't passed "link juice"), though they can be a good source of click through referrals. (If you want to keep track of them and have a record of their changes, you can manually add such links in your Monitor Backlinks account though.) You can verify whether the link is being dynamically generated by using an "html source code viewer" (there are many freely available if you search for them.)

If you'd like to see more than 1 link per referring domain, then please follow the directions in this article: http://intercom.help/monitor-backlinks/advanced-questions/i-am-using-the-default-setting-of-showing-one-link-per-referring-domain-how-do-i-change-it-to-see-more-links-per-referring-domain

Please note that you can also import backlinks from other sources (like Google Webmaster Tools) into your Monitor Backlinks account: https://blog.monitorbacklinks.com/guides/how-to-import-links/

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