Not to be critical but in my experience customising CSS (including theming) or/and using extensively rich markdown plugin messes up the presentation of gutters (narrow vertical line).
I'm not sure that this is your problem but in my experience it usually is. Every time I change css I try to catch if gutters were screwed up.
It takes a lot of fiddling to make it work "just right" on all window sizes, themes, alongside other editor plugins, etc.
For now, you may list plugins you use, attach the screenshot how does this narrow vertical line look like, show your CSS (Settings - Appearance - Show Advanced - Joplin-wide settings) and, if you're technical enough, this css line might help, adjust it to your situation:
.CodeMirror-gutters {
/* locates the gutter more or less to the left */
left: 1px !important;
/* makes gutter colour to be transparent essentially hiding it */
background-color: transparent !important;
}
P.S. I don't know much about css, this just happened to help in my situation, so if I'm wrong, pm is welcome