Stars wanted to sign Mncwango on a season long loan deal, but the Clever Boys are not interested.
The former Polokwane City striker only played only two Absa Premiership matches, and one Nedbank Cup encounter since joining Gavin Hunt’s side from Rise and Shine in January.
Eymael, who previously worked with the striker at City, initially wanted Mncwango to replace Siphelele Mthembu who left for Cape Town City.
But Wits' reluctance to part ways with the 30-year-old saw Ea Lla Koto settling for Cape Town City forward Judas Moseamedi, who has joined the Bethlehem based side on loan for the season.
"We asked him Jose [Wits CEO Ferreira], but unfortunately we couldn't make a deal," Eymael tells KickOff.com.
"I don't know exactly why, you have to ask Rantsi [Mokoena] and Jose why we couldn't make a deal. And the guy he wanted to come here, but now it's okay we finalised with Judas Moseamedi, and we are happy with Judas.
“It's unfortunate for Thobani, but what can we do? It's like that you know we tried to make a deal and Jose couldn't agree with Rantsi about the deal of Thobani for the loan...and so it's something like that what can we say?"
Ferreira couldn't be reached for comment.