If you have ships from multiple factions (ie, TEC and Advent) all of there phase space effects default to the faction the player is playing as, example if playing as TEC and you have captured advent ships, there phase space effects become the same as other TEC ships that where not captured (ones that you built).

Not sure if this was meant to happen, but after seeing the end of the full intro video with all the ships having there normal phase space effects, I thought it may be a bug.

As seen at 2:50 each ship has there own original phase space effects.