"We don't want to stand in his way," Smith said. "But when I saw he had already played for Waitakere - it was that horrible feeling.
"Nobody likes being made to look silly, for the sake of a two-minute phone call, so yes, it has left a slightly sour taste."
Waitakere were under the impression Manko had informed Smith of his intention to play in the Phoenix A match - but that was not the case.
However Smith said Waibop United would not enforce a stand-down period on Manko.
Under the standard premiership player agreement, Waibop could insist upon five week's notice in writing prior to releasing Manko - or seek a transfer fee.
But Smith said it should also be acknowledged Manko had worked very hard for Waibop on and off the pitch.
"While I'm disappointed, overall Maksim has been a great lad, a real team player, and this episode has been out of character.
"We understand the difficulty of travelling from Auckland and why he would want to take an offer from Waitakere, so at the end of the day he will go with our blessing."
Meanwhile Waitakere will also sign Allan Pearce - the all-time top goalscorer for the premiership - next week, after he was unavailable at the start of the season.
And Waibop are set to announce the signing of former New Zealand U20 and Team Wellington striker All White Ethan Galbraith, along with former Waikato FC striker Sam Messam next week. Messam has most recently been playing in the New South Wales Premier League.