Which version of Skill Core are you using? I was under the impression that Yanfly was correctly returning the width of the skill cost display (which is entirely necessary for the display to be correct).
EDIT: At least at a glance, Skill Core 1.13 looks compatible. Make sure you're updated! Also, make sure this plugin is BELOW Skill Core on the plugin list, as well as all other plugins that modify skill cost in any way.