Bags in Transit

I have been on an international flight to Namibia. I traveled from Port Elizabeth to Johannesburg and from Johannesburg to Windhoek. When I went to Windhoek every thing went smoothly. I did not need to collect my bags before I arrived in Windhoek. Going back from Windhoek to Port Elizabeth was another story. They claimed that I had to collect my bags at Johannesburg which resulted in me being late for my flight back to Port Elizabeth. I had to pay R 1286 for another ticket and R 1 727.10 for accommodation at the City Lodge in Johannesburg as there was no flight left in the same day.