I even filtered brand and non-brand keywords to see clicks. Suddenly i realized, that the whole amount of clicks shown by GSC is much higher, than the sum of brand and non-brand clicks.
Why is it so?
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Discrepancies between chart totals and table totals You can see differences between the chart totals and the table totals for several reasons: ... When filtering by page or query, the "matches" and "does not match" totals might not add up to the unfiltered total. For example, adding the totals for "Queries containing:mouse" and "Queries not containing:mouse" might not equal the total values when no query filters are applied. This is because anonymized queries are omitted, and data is truncated due to serving limitations."
I have the same problem. GSC reported 6,500 total klicks, 2,500 with brand-keyword, 500 without. So I am missing data for more than half my traffic. Seems like we can do nothing about that.
Also you can look at this thread here where they discuss the same problem: https://support.google.com/webmasters/thread/4924855?hl=en