Does SPFx colors affect the SharePoint Site theme

From yesterday i am seeing the issue on the Site theme.

I have SPFx extensions and webparts deployed in the sites and both framework uses the custom color built in the .sppkg package. And I have custom site theme installed using PowerShell.

Does the SPFx color scheme affect the SharePoint custom/inbuilt theme? As of now, I see the difference when I select the dark blue site theme. The SharePoint site pages and webparts are showing blue and white colors.