Lately I've had a couple of multi-stage quests seemingly get completed by my party of two toons, but once we finish up the ground portion and leave the system, invariably one of them somehow didn't get credit for the last portion and has to go back and do that part again, even though every step of the way they were getting progressed. Any idea as to why this is happening, or is there something I'm missing? It happened most recently on the 'Treasure-Trading Station'.
Ive run into this problem myself. and what Ive found is if you just let one character forge ahead and do not do the general tasks with both characters then the one that did not compete the general tasks will not register as completing the mission.
For example, you have a mission where you have to talk to officer a and officer b and kill 10 enemies. If one character talks to a and b but the other doesnt and they do kill the enemies, the one that spoke to a and b will get the credit for completing the mission but the one who did not wont get the completion, even though the screen shows it completed.
It sounds from your your post your running two at once. if you set one to follow and dont complete the tasks with him he wont get the credit since toon 1 is doing all the work.
This is a pain sometimes as I run a lot of missions with my fleet and we have a few gung ho individuals who just run forward and complete the mission. so when its over they get the credit but because by the time I got to the objective, its completed and I dont get that option, I dont get credit for it, and then have to go back and run it again to get the credit.