@SethStorm666 is right: you likely have a theme you brought into this.
What you need for Budgie when this happens is gnome-control-center
or gnome-settings
(I forget; I'm at work) from the repo. It has a 'master' force-every-single-thing-to-dark-theme button. I don't know if this is Solus-endorsed or even 'best practices' or even real solution---
---but it's always worked for me when that horrible 2-tone window, or one-is-dark-and-one-suddenly-is-light sh** afflicts the desktop.
*another solution is just to be happy with the base themes in the repo. I still alternate Qogir, materia. zukitre, Arc-D etc etc. edit/typos galore I need to trim my fingernails