I couldn't see any way to identify a timed quest so when I ran into this problem which I admit was a PITA I decided to only have one side quest active at a time and concentrate on completing it. I don't know if it's related but I don't seem to have the same issues with broken quests as some so maybe it's better not to have too many active at the same time anyhow.timed quests in this game are so badly done it isn't funny.