Why are there differences between Google Analytics And Google Webmaster Tools in external links data? Generally this data do not coincide with each other.
Google Analytics and Google Webmaster Tools are collecting different kinds of data, and they are sampling the data differently. That's why it's different.
Google Analytics "Referrals" measure a person who clicks a link to get from the external site to get to yours. Their browser must report that referral via
Google Webmaster Tools "Links to Your Site" measure links to your site that the Googlebot spider finds when crawling the web. That is entirely different than what Google Analytics is measuring.
Also, neither Google Webmaster Tools nor Google Analytics will ever give you exact numbers. Both databases contain a ridiculous amount of data, so they need to sample it. You're supposed to be looking at this sampled data for trends over time to see if your marketing is helping or hurting your efforts.
Also, I've had this suspicion that Google never really wants to give you all the data. They ultimately don't want you monkeying around with your SEO too much because it undermines what they're trying to do in providing objective, relevant results.
The difference is because Google Webmaster data is updated monthly whereas in Google Analytics you can see the daily activity.
Google webmaster tools has all the data, even if it does shows in Webmaster dashboard
Check out the following links to see the answers from the Google itself