The Buccaneers staged a second-half comeback to defeat the Team of Choice 3-1 for a spot in the quarter-finals on Saturday evening.
Middendorp claims he did not expect Lungelo Bhengu to start cramping so quickly after the halftime break.
"As long as we were capable to keep the structure, to do right what was planned, I think we were good in the game, one or two moments in the first-half we could have taken the second goal," Middendorp told SuperSport TV.
"I was not expecting that six or seven minutes in the second-half somebody starts cramping, we spoke at half-time, be responsible, if something is not right, we change now good.
"But that's probably the right of a young player, that's definitely disappointing because in this one-man down period we conceded these two goals, ja it's definitely not the way we wanted, but good we take it.
"As a I said before for us it's very crucial to see the bigger frame in terms of the league going towards the next games, sort it [until] the end of the season, end of May.
"We had a number of players in the PSL in a competition like this, we got an indication that some will work, some will need a little bit more time. A number of players who could be in the starting XI are not in the field today for different reasons. Good, we start working on it, continue, our next game is definitely crucial."