Flagged passport

We booked online with Flight Centre to fly from Cape Town to ****et. Flight itinerary was Cpt to Jbg, then Abu Dhabi, then ****et. Upon online booking, passport numbers were asked and obviously given. We checked in yesterday (with our passports) the 23rd at CPT to fly with Kulula to JBG. Luggage booked directly to ****et. No problem. Got to JBG and on check in at Etihad airways, I was told my passport is flagged which meant that we couldnt leave the country! Im obviously taking this up with Flight Centre, but now I want to know why my passport flag didnt come up with checking in at Kulula either? Luggawe was booked ON MY PASSPORT to ****et! Nevermind that it was a domestic flight! Home affairs blocked my passport after I was in a smash and grab in Dec 2017 and my TEMPORARY passport was ******! (Not valid at the time as I had my original at home) but still thought to rapport it with the rest of what was ****** (my handbag) My original passport is valid until 2027 so if Flight Centre, or Kulula dont check it, how am I supposed to know that it is flagged? We had to buy MORE tickets to get us home from Johannesburg last night! This could have been prevented if it was picked up in Cape Town already!