This happened to me just last night. Went in, got the CS, warped out and Zubaba would just tell me to go to Inner Horutoto.
Went back to the gate (thanks Elonmusk!!), clicked on the gate and got the CS again. But then, just to test, clicked the gate once more and got the CS again. I did this a couple of times and was always able to get the CS. No interruptions or anything. What I noticed is that the temp KI for the CS, Charm of Light, didn't disappear. When you click on the Gate of Light, a message says that the Charm of Light breaks, or disappears, or something. This is what I believe is the cause for getting stuck.
I logged off and logged back in, right there, in front of the Gate of Light. Clicked on it and got the CS, but this time, the KI was removed from my inventory and when I clicked on the gate again, no more CS. I got only a message saying the gate was firmly shut. I spoke to Zubaba and got the correct CS and completion of this mission. Traded a rolanberry to the other NPC and got the charm to open the 3-mage door.
If you run into this bug, do this *before* you warp away from the gate. Make sure the temp KI is gone from your inventory and that you don't get the CS again if you click on the gate of light.
Hope this helps!