You had mod_php when you created those virtual servers, and you shouldn’t have.
Now you don’t have mod_php (which is great!), and so you need to remove all that mod_php crap in your Apache configuration.
I believe if you do Re-Check Configuratioin, and then change the execution mode of all of the problem sites (and then change it back…PHP-FPM is the best execution mode for nearly everyone) will cause Virtualmin to fix this for you. But, you can also just delete all the php_value nonsense from the file (that’s a lot faster than clicking through every domain).
It may be that Validate Virtual servers can also fix this, I’m not sure.