Deeply hidden T's and C's

Booked a flight to Germany via ebookers with Austrian Airlines and Lufthansa. I unfortunately could not make the one flight from Berlin-Vienna-Hamburg. One week later I then had my flight back home from Hamburg to Johannesburg. When I tried to check-in my reference/booking code could not be found. I had to go to the airport only to find out that my entire international flight back home was cancelled because I missed the one flight a week ago. I would have to pay a 3000 euro fee if I would want to get back on the same flight. No communication on this at all from airline or Ebookers! Lufthansa help desk was so unhelpful and not accommodating. This info is nowhere to be found on the itinerary, their website or the airlines websites. Was forced to buy another ticket back home at the last minute. Totally unacceptable as a flight booking agency and the airlines to not communicate this beforehand.

Apparently this is common practice for Airlines to do this? But if you're booking through a flight agency or third party website how do you as the customer know this if they do not clearly highlight this or bring it to your attention? How is it ok for an airline to completely cancel a flight because of one missed flight over a week ago and that has already been paid for without letting you as a customer know at all? Saying that it's part of the T's and C's (which is definitely not upfront or clear) is definitely not a good enough answer.