In addition to the September call-ups, the Rays also activated Jeff Niemann from the disabled list. And to make room on the roster, the Rays designated Will Rhymes for assignment (via Marc Topkin). Rhymes will now have to clear waivers in order to remain in the Rays organization.
Players on the 60-day disabled list do not count against the 40-man roster. So even though Niemann was already on the 40-man roster, he was not taking up one of the 40 spots. Hence a player needed to be cut.