Apache log imports importing only small amount of logs?

Elastic Stack Logstash
5

Not sure about updates but there's a docs.deleted which is high? See:

health status index               uuid                   pri rep docs.count docs.deleted store.size pri.store.size
green  open   .kibana             MPxywALaTHmN8j5v1fZ68A   1   0          2            0     12.6kb             12.6kb
yellow open   logstash-2017.12.16 40M-4BFHS4iUXuAjyDH7sA   5   1          1         2175    755.7kb        755.7kb
yellow open   logstash-2017.11.12 lGQD5y3uSiipb9DyrGlb2g   5   1          1         1461    530.5kb        530.5kb
yellow open   logstash-2018.02.10 zdEixWK0RqCuULTmPUaFCA   5   1          1         2598    924.1kb        924.1kb
yellow open   logstash-2017.11.07 9wLi8LMqRJyKcJHoVkh09w   5   1          1         1305      504kb          504kb
yellow open   logstash-2017.12.05 8gxkxww7TBmgCmUr-SJvmA   5   1          1         2154    665.6kb        665.6kb

and so on and so on... Is this caused by the documents being updated and if so, how would I prevent this from happening?

Thanks for your patience =)