I've just logged in for the Pi Canis missions, and out of 6 warp-outs, 4 times the trails were romulaney green, twice klingon red. So the last, May the 3rd patch didn't fix it.
I've tried both the mission offered warp-outs (offered in a dialogue contact after finishing all of the mission's objectives) and the button on the minimap. Doing either sometimes resulted in red trails, sometimes green trails. In other words, I have no clue what decides on the color.
TOIVA, Toi Vaxx, Toia Vix: Bring in the Allegiance class Toi'Va, Ti'vath, Toivia: Design that long overdue Tier 5 C-Store Raptor Tae'Va, T'Vaya, To'Var: Give us Asylums for Romulans