I worked and drilled the question and I find that in Ecoinvent 3.12 library downloaded from Nexsus and library created from Ecoinvent 3.12 database without modifications there are two strange things.
In processes in both libraries
market for used railway track | used railway track | Cutoff, U CH and
treatment of used railway track | used railway track | Cutoff, U
have in output two times the flow used railway track.
But in the same processes inside Ecoinvent database the flow "used railway track" appears in output only one time.
I corrected in the libraries and the result now differs only for 0,21% - in real world nothing.
I think it's the problem in creating Json file during library creation.