Suddenly, some of my themes have stopped behaving correctly and are not loading in correctly. When I check the console, I see this error "Uncaught ReferenceError: ThemeScripts is not defined".
Most of the CSS is just not loading in, what can I do?

You could start by giving us a hint about what LimeSurvey version you are using and what changes you have made to the system.

Oh yeah, I'm sorry. Version 4.1.0
The only real changes I've made to the system are CSS changes to the login and main page, but these errors are with survey themes

LimeSurvey 4.x is not entirely stable. Try updating to the latest version and retesting.