It appears when I go soloing on a mission that takes me to X planet or X base, I can continue as normal. But when I try to beam out (If the server is lagging) it begins playing up. This leads me to believe that Quest instances are actually based on your own system (When solo) not on the server. This has caused me to have to repeat the same quest multiple times, especially lately with the server lag. I could be wrong with this theory, just saying that's what it seems like to me.