I have been searching for why this happens for some time, and I can't find anyone else who has my problem. Sometimes, Godot's user interface changes to different colors:
Everything in this window has a gradient on it, going from black to blue. This happens seemingly randomly sometimes while I'm working, and doesn't go away until I restart Godot. I am using Godot's default theme.
It has happened with different colors as well, such as yellow and blue.