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To be clear, you shouldn't put files in your site's root. It's bad practice. Joomla has specific locations where web accessible, static media files can be located in e.g. your template's folder or the media folder.

Your problem is that you put the file in the site's root which is the stone age approach. The correct approach for over 10 years no is to use link elements in your HTML output to explicitly reference the various sizes and formats of site icons so that different browsers on different platforms can find the correct one.

Please do bear in mind that the default rules in Admin Tools' .htaccess Maker do make it possible to have your site's icons – even in the legacy and discouraged .ico format – in the folders Joomla allows static media files including the folders I already mentioned above.

Adding automatic exceptions is a terrible idea when transferring sites among servers. Many servers come with a small set of preinstalled files, one of which is a favicon.ico. Sometimes permissions issues make it impossible to overwrite them on backup restoration. It is therefore possible that by adding an automatic exception we'll make your site serve that default icon instead.

Here is some more in depth information on the subject of site icons in general and how to reference them in your HTML output: https://www.emergeinteractive.com/insights/detail/The-Essentials-of-FavIcons/