Munyai missed the league game at Loftus Stadium on Wednesday night as his side lost 2-0 to Mamelodi Sundowns.
Lidoda Duvha have not played midfielder Phathutshedzo Nange ever since Bidvest Wits announced his signing on a pre-contract, and Munayi could suffer the same fate.
Nange and Munyai's reluctance to renew their contracts with the Limpopo-based side and their signing of pre-contracts with other PSL teams seems to have not gone down well with the club management.
Leopards coach Dylan Kerr preferred not to comment about Munyai's absence against Sundowns but voiced his disappointment towards his captain for not being honest about his move to Highlands Park.
"That's the club's issue. The chairman [David Thidiela] is the person to speak to about Marks [Munyai]," said Kerr.
"Obviously from what I have been told he signed a pre-contract with Highlands Park and the way he has done it in football terms, I believe it's wrong. He should have been honest, open and straightforward."
Polokwane City striker Rodney Ramagalela is another player struggling for game-time after signing a pre-contract with The Lions of the North.
Ramagalela has since been suspended by the club but has not yet been charged or faced the club's disciplinary committee.