I went back to older posts here and found that most people had the same problem, while a few others didn't. I have the same problem and have played through the mission a few times.
I decided to set up a little "experiment" and positioned scouts near all 3 of the locations where the probes spawn. I destroyed them before the vagyr carrier jumps in, and the objective is marked completed, with fleet command saying they were all destroyed and to stay on high alert. I got the "enemy emerging from hyperspace" message twice soon after with nothing actually emerging from hyperspace. The vagyr carrier jumped in later and I destroyed it, along with any probes it dropped, and then all was quiet again. Still stuck.
I think that the problem/glitch/whatever has to do with the 3 carrier hyperspacing in, not the actual objective, because I did the objective and I'm still sitting here twiddling my thumbs. I still got the "enemy units emerging from hyperspace" message that everybody gets if they wait long enough, but nothing happens.
BTW, I did reset the campaign as somebody suggested, nothing changed when I got to this mission.
Annihil4t0r
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