Batch injestion vs Kafka realtime + re-index. Segemnt file size

For some reason my segment file sizes differs a lot when I use diferent indexing methods.
What could be the problem?

When I use kafka indexing service with re-indexing task to minimize shards count - one week segment is 632 kB
When I use batch injestion task(firehose) - one week segment is 15.9 MB

Queries shows the same results on both segemnts.
Segment(WEEK) and query(HOUR) granularity are the same for both methods. rollup set to true.
I tried to re-index segments with same task as I used to re-index kafka segments but with no luck.

What am I missing?