Sum of branded and non-branded clicks is much lower than the total reported by Google Search Console

Discrepancies between chart totals and table totals You can see
differences between the chart totals and the table totals for several
… 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: