its very likely that somewhere in your theme, perhaps in your navigation or footer, you are linking something like
<a href="https://wordpress.stackexchange.com/questions/254739/Contact-Us">
which will then link to the subdirectory.
You need to find those issues and fix it with something like
<a href="https://wordpress.stackexchange.com/Contact-Us">
or
<a href="https://wordpress.stackexchange.com/questions/254739/<?php echo get_site_url(); ?>/Contact-Us">
Without seeing code, it’s hard to tell though.
Have you done a view source on your product page?