The idea is simple, Obito has been drumming up Sasuke's hatred towards naruto for a while and he even suggested given Itachi's Eyes to him after his overuse of his own MS, which he did take.
Obito took Madara's Right eye and give it to Nagato, being of the Uzumaki clan he was genetically capable of using it. Nagato was seen resurrected having missing his right eye but Itachi's Eyes were still intact. To me, this suggested that one Eye was given to Sasuke and the other to Nagato.
While at the time of reading this, I cannot flesh it out due to time restraints, feel free to shoot it down or expand on it