There is a basic SEO rule: content should only be available via a single URL on your website. There are some legitimate reasons to break that rule. If that happens, you need to take additional action such as use the canonical tag to identify the primary page.
Your home page situation is NOT a legitimate reason to break that rule. It's poor web design. It needs to be fixed. OSE is doing its job correctly. OSE is calling your attention to a SEO issue which requires your attention.
SOLUTION: Remove all references to the /index.php page on your site and replace them with the / page. Also add a 301 redirect from the index.php page to the / page so anyone who bookmarked or linked to the /index.php page is seamlessly taken to your home page.