What happened to the tomoe in Sasuke's Rinnegan?
The latest manga of Naruto Gaiden: The Seventh Hokage, show us that his eye was weakened and that's why he didn't have tomoe in his Rinnegan or why he couldn't activate his Eternal Mangekyō Sharingan.

It was weakened because he tried to open dimensions with his eyes which consumes a lot of chakra, as Obito had tried before he died in the battle with Kaguya.