Hi,
First of all, according to Google's recommendations, canonical links should be absolute (not relative). Keep this in mind ;) so the 1st one is correct, you should get rid of the 2nd one.
Anyway, because Joomla & Virtuemart are already taking care of the META tags insertion; we don't manipulate the meta tags within our extensions. In MaterialMart, there is no line, not even a single one, to add/remove/edit or rewrite any mateTag's (including canonical)
So, i believe this duplication is caused by something else (most likely by a plugin) -- definitely not because of MaterialMart, i can assure you about that.
Regards.