Impossible to say without seeing examples of the HTML+CSS + maybe showing some screenshots of the problem.
You could also use the Calibre plugin, ScrambleEbook:
https://www.mobileread.com/forums/sh...d.php?t=267998
in order to create a sample file we can mess with.
I am going to take a stab in the dark and bet there is some CSS letter-spacing shenanigans going on.