I'm just doing some SEO using Google's webmaster tools and have come across something a bit strange on some occasions people seem to be getting to links like:
probably because they take a guess at 'lets see if this domain has an index.php page' so the robot downloads index.php and find all these links like store/view-products/my-product and since these are relative links (don't start with backslash) then the search engine trys index.php/store/view... etc and gets back valid content.
Ideally, what you should do is put in a route to redirect (302) index.php to / .
If this is difficult, perhaps just put / on the front of all your links.