Obviously since / and /index.php use the same files, the meta tags would be the same but I was wondering if there is anything I should do about it. Is it ok for Google to think they are duplicate? Just being safe. Thanks.
From an analytics point of view I don't think there's any danger, but it would probably be nice for you to have that data all in one place? It would make reporting much easier - esp. more complex stuff like path analysis.
From an SEO point of view it would be much better for you to only have one version of your home page. I would be looking to 301 redirect any requests for /index.php to /. You could do that quite easily using .htaccess.