Only in the case where the lower cost is for a strip with stops. I have never seen a lower price non-stop return flight be listed lower on the page. And I'll go ahead and say it would be very rare for a EWR-FLL itinerary with stops to come in cheaper than a non-stop.
I have seen a lower price 1 stop(all my flights are one stop unless hitting connection to IAH only) a number of times lower on the page.