Elasticsearch index has multiple document ids

Hi.
I am using Logstash / Elasticsearch (8.5.3) and am indexing json data.
In logstash I use http input plugin, filter plugins and elasticsearch output.

Currently the auto generated @version field in logstash filter is removed and document id in elasticsearch output is my custom and unique id.

I displayed the index in kibana discover and noticed in field statistics that the count of my custom id is 5000 and the distinct values are 4950.

I suppose that since I removed the @version in filter, elasticsearch indexes the same document id (custom id) more than once, although they are just updated custom ids are.

Can it be the reason?
Thanks

Can you share 2 documents with the same "id"

Also, can you share your logstash.conf

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