Issues with Seat Selection and Service on Turkish Airlines Flight

I live in Antofagasta, Chile. My wife and my 5-year-old child, who has been diagnosed with autism, and I had to travel to my family in Izmir. Due to the transit visa requirements in Europe, we decided to fly with Turkish Airlines for the first time and bought Sao Paulo - Istanbul tickets. Because the ticket prices were very high, we purchased our tickets for June 14 - July 7 in April through an agency with an installment plan. After the purchase, we received an email from the agency stating that we could select our seats, and we reserved our seats on the Turkish Airlines website. There was no issue with our flight to Istanbul, but when we checked our return tickets, we saw that our seats had been changed and we were seated separately. (The seats we selected were sold to others without informing us.) When we went to the Turkish Airlines office, they told us that their system changed at the end of June, and we would need to pay extra to select seats or request seats during check-in. How can they cancel our right to select seats without informing us, especially since we had already chosen our seats? Moreover, we are a family of three, it's a long flight, and most importantly, our child has autism. I can't imagine the problems that would arise if we don't fly together. Additionally, they did not allow us to check-in 24 hours in advance because we bought our tickets through an agency. We contacted the agency, and they told us to check-in at the airport. Now, at the airport check-in, they are saying that all seats are full and have separated us into different seats.
I think this will be my last long flight with Turkish Airlines. I had previously flown long distances with Turkish Airlines to Hong Kong and Thailand and had different issues. It's better with KLM or Air France. I have had more than 10 transatlantic flights with them and never had any problems. Also, the Turkish Airlines flight was delayed by 1 hour and 45 minutes, and I had to change another flight with a different airline, costing me an extra $150.
So, I spent around $1500 per person and, thanks to Turkish Airlines, my family and I were left in distress.