If you take special relativity literally, any object observed to be travelling faster than light in one frame can be shown to be not moving(in time) in another frame and traveling backward(in time) in a third frame.  Any universe that features faster than light (FTL) travel does not use the physics of our universe. Or if it does, it has to deal with the time travel aspect of FTL travel.  

It's safe to say that either:

1) The mass effect speeds are not **really** faster than light speeds, but only talked about that way in-game.

**OR**

2) The physics of the game universe are not the physics of our universe.