For my upcoming trip, after reading this thread, I did attempt to use an online booking agency for my flights when my attempts at booking directly through the airline's website kept giving me issues. I kept getting an error.
Expedia gave me the same error - could not confirm the flights.
Unfortunately, I ended up having to call the airline directly. But, I did find out that Lufthansa at least has awesome customer service in that the agent tried his darnedest to get me the right flight for the right price - was on the phone with him for 45 minutes start to finish.
Wasn't very convenient and unfortunately did end up costing me some additional dollars to get the right flights for my trip. Ultimately, the issue was with partner airlines being booked and their respective communications had not been updated. I would have likely spent the same amount in the long run had I picked the right combination online.
But at least the agent proved that customer service isn't a completely dying art. That's something.