Premier League leaders City had a £47m bid for the Portugal international, 25, turned down last week, but feel Wolves' valuation has become unrealistic.
Midfielder Nunes has been absent from training recently.
"He's not with the group at the moment, his choice," said O'Neil.
It is understood Wolves want in excess of £60m for Nunes, who has made it clear he wants to join Pep Guardiola's side.
O'Neil, whose side beat Blackpool 5-0 to reach the Carabao Cup third round, added: "After the bid from Manchester City he decided it was best for him to not to be with the group. Club policy, and how we deal with things like that, is set in place.
"As far as I'm aware there's been no improved bid. Matheus Nunes is still our player, we have a long contract still with him and at this moment I fully expect him to be here come 2 September.
"The next few days will be key of course and conversations will take place that will be private between me and Matheus and I'm sure the situation will be resolved."
West Ham's Lucas Paqueta was always City's first choice to strengthen their midfield and there is the possibility they could go back for the Brazilian in January if betting allegations against him are resolved satisfactorily.
Wolves are known to be interested in City midfielder Tommy Doyle, 21, but that will only happen if Nunes moves the other way.
The Midlands club signed Nunes on a five-year contract last summer, paying a club-record £38m to Sporting Lisbon.
He was a key figure during the second half of last season as Wolves successfully avoided relegation, finishing 13th in the table.