Ntseki's relationship with Zungu has been scrutinised ever since the former Mamelodi Sundowns midfielder was snubbed for the Bafana Bafana squad named back in March.
Zungu went public to voice his displeasure at the decision considering he is one of the country's finest talents playing in Europe, now playing under Liverpool legend Steven Gerrard in Scotland.
Ntseki said ahead of Friday's Africa Cup of Nations qualifier against Sao Tome and Principe that he never had issues with Zungu.
"The question of Mr Zungu, I don't know, but I know why there's always an issue with Bongani Zungu," Ntseki told the media.
"Bongani Zungu was excluded from the team like any other player, but the unfortunate part about that situation is that the media and everybody reacted.
"Because when somebody is not included there's always disappointment. In expressing how disappointed you are, it ended up being an issue, of which there was not any issue between Bafana Bafana and Bongani Zungu."
Ntseki said if he were to start having personal issues with players, it would mean he does not deserve the job of national team head coach.
"I kept on saying if I were to have issues with players that are not selected, it means I don't have to be Bafana Bafana coach, because every player in this country is eligible to play for Bafana Bafana and if you come in and start having issues with players, that means you are not patriotic," he continued.
"And being a coach that has come from the junior ranks, dusty streets and from the villages, today becoming a Bafana Bafana coach, from that experience and process of getting matured and empowering yourself, I think I've worked with a number of coaches and I have learned a lot from them, and now it's my time."
The national team has always had a strained relationship with Europe-based players who command high salaries, with the Bafana head coach needing to have the skills to deal with overseas stars.
Ntseki says is critical for him to manage the situation well and for those players to focus on the most important thing, which is representing the country.
"The question is, how do you handle yourself, how do you manage the situation? You are dealing with billionaires and millionaires here that are playing for Bafana Bafana," he quipped.
"The most important thing is, how do you manage them, how do you make them a team and go in there and fight for the country to make them proud?
"If we lose, I'm the one to be blamed. I'm the most-sought-after coach in the country and even in the world.
"So I think Bongani Zungu is looking forward to the game. We spoke over the phone, he played last weekend and will be more confident coming to the team."