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Please explain the situation presented in the following screen shot from the WMT SR clicks statistics. If it says "100 clicks" on the given date, why in the chart there present only 7+3+1+1=12 clicks?
Why there is a "contradiction" when I ask to see clicks from the last 28 days?
In all likelihood, the keywords that you are getting from Google are (not set) and cannot be shown to you due to privacy reasons or are too low in search volume to be included in search tools.
Admittedly, your ratio is incredibly low (12%) where it should be in 40-60% when normalised for volume, so try increasing your date range to 90 days to see if you get more usable data.
It isn't a contradiction, those clicks exist: simply choose pages instead of queries in the top to see how it breaks down on a URL basis. Google simply choose not to or cannot show you those keywords.
Be sure to connect Google Analytics and Google Webmaster/Search Tools so you can see this (not set) data and see how much of your search queries are in this range.
Edit: You can learn more in the SEO Reports section in the analytics help section.
Relevent Text:
To protect user privacy, queries that are made infrequently and queries that contain sensitive or personal information are grouped together as (not set).
