I had something similar happen to me as NCN616 reported above.
I had a hunt mission and upon completion it kicked off the next mission (Probe Rikti minds) and then Investigate Rikti base from Steve Sheridan). I completed the hunt mission in the Rikti war zone and the next mission appeared but no zone as to where it was. (talk about secret bases!). GM Willow replied to my petition: Some of these aren't particular about where you complete the hunt missions but upon completion, when selecting the following task, tend to go a little wonky when doing it from an opposite or cooperative alignment zone. I had that happen the other day with a redside contact, I had been picking up badges blueside (as a rogue alignment) and the contact issued me a door in Skyway. Of course, the door was broken, but returning to an appropriate zone fixed the issue.
In my case, I tried a few zones to see if the mission would give me a door but had no luck. I ended up abandoning the mission and picking it again. I went to Crey's to beat on Rikti and the following mission appeared in that zone.
Cheers,
Parenthetical