The dark system theme I have set seems to make some applications look funny, with dark boxes where they should be light. Is there any way I can manually set a theme on a per-application basis?
I had this problem, and it was definitely a theme issue.
https://askubuntu.com/a/1372318 may be helpful in setting a theme just for libreoffice, it you're using GTK themes. (Basically, override the GTK_THEME variable in the .desktop file). I haven't tried it myself since I just switched to a different theme.