ES and kibana documents count difference

I have 5 million documents in two indices and one index pattern on both of the indices in kibana. e.g: Index1, Index2 and index pattern Kpattern.
Kibana is showing total count of 2.5M only while it should be same as ES (5M). What could be the issue as everything seems to be working fine. One more issue I am facing is performance tuning for the historical data. Whenever I try to create a visualization request times out because of too many documents. I have followed the tuning guide on

Can be a date selection issue may be. Hard to know without details.

Anyway I moved your question to #kibana

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