I've thought about it some (IDK the answer). I cant remember, was Bates starting before the injury to Morse?
If so, here is my best guess. With Feliciano just coming back from injury (and I think I heard somewhere during the postgame show that it was possible he was going to be on a pitch count before the game started), would it be possible that Bates then would have been the only other player who could play C? If that's the case, maybe they put him on the bench after that series to prevent some kind of weird nightmare scenario where if Bates gets hurt and Feliciano gets hurt/reinjuried/pitchcount then they would be without a C.