The lanky forward was suspended by City last season for comments he made in the media after interest from Pirates surfaced.
Mncwango, who then seeked help from the South African Football Players Union (Safpu), confirmed that the Rise and Shine management had suspended him.
However, Molekwa has claimed that he is unaware that the former Baroka FC frontman was sidelined by the club midway through the season.
“I don’t know about the suspension,” Molekwa told The Citizen.
“The management never told me that Thobani Mncwango was been suspended," he said.
The 29-year-old Mncwango was first linked with Pirates after netting 13 goals in 22 PSL matches for Polokwane at the end of the 2015/16 season.
“Sometimes it is difficult for me as a coach to change a winning team. I believe we work as a team and not as individuals," he continued.
"I know he was expected to be in the team but we pick the team based on what we see at training," the retired player explained.
Molekwa, who was recently appointed permanent City head coach after serving as a caretaker coach, stated that his side will play good football in the new season.
“Football is about results. We can play good football but if the results are not good then it doesn’t help," Molekwa stressed.
"We have to play to win. We have to work together to ensure we continue to do well. We will remain grounded and play for the result," he concluded.
City will make their debut appearance in the MTN8 Cup when they face Cape Town City in the quarter-final clash in the Mother City on Saturday.