If you've played the older games, Me Ga Au Toki is written as 目が逢う瞬間(とき)(Me Ga Au Shunkan(Toki)). Therefore, it is pronounced and also romanized as Me Ga Au Toki.
Better explanation (For those who understand Japanese terminology): Shunkan has the furigana toki written above it (or to the side in parentheses in the game lyrics), which gives it the pronunciation toki despite it being written as something else. This can be seen in iDOLM@STER 2 with the song Little Match Girl; Heroine is written as Protagonist, with the furigana giving it the pronunciation heroine.