After some tests I have found problem.
The problem lied step before → reading database and write it into .pbf file using osmosis with granularity=20000 parameter:
(osmosis --read-apidb host=$DBHOST database=$DBNAME user=$DBUSER password=$DBPASSWORD validateSchemaVersion=no --log-progress --write-pbf file=$FINAL_PBF_NAME omitmetadata=true granularity=20000)
As osmosis documentation says:
The granularity or precision used to store coordinates. The default of 100 nanodegrees is the highest precision used by OSM, corresponding to about 1.1cm at the equator. In the current osmosis implementation, the granularity must be a multiple of 100. If map data is going to be exported to software that does not need the full precision, increasing the granularity to 10000 nanodegrees can save about 10% of the file size, while still having 1.1m precision.
I don’t need such a accurracy that’s why I used 20000 (2,2m precision).
Maybe you will better predict what happened.
Perhaps during truncating accuraccy of points, some crucial of them overlaps? Maybe as warning says → weight of the edge between 2 nodes are less than 0.01. (I assume that distance can be took as a weight in i.e. dijkstra algorithm).
However I will omit granularity parameter.
Thank you very much for your help!