The Techiman-based side's hopes of causing a shock away in Kumasi ended in disappointment following a 1-0 loss in the Zone A matchday 11 fixture.
The goal came in the last quarter of the game when referee Bismark Appiah pointed to the spot after a foul. Abdul Ganiyu stepped up and expertly converted the penalty to seal all three points for the second-placed Porcupines.
"There is no fairness in this part of the world because the game was balanced in the first half but there was much pressure on Kotoko due to their recent performance [and that may have resulted in the referee's decision]" Adipah told Ash FM.
"Tactically, [Kotoko found out our strategy] in the first half.
"We wanted to take them on in the second half but the unpardonable penalty changed everything in the game.
"It's very painful that these young players exhibiting their talent against Kotoko would lose the game with such decisions but we have accepted the defeat in good fate."
Wonders, who next play Aduana Stars, are sixth on the table ahead of the final two rounds of matches.
Only the top two at the end of the first round will progress to the next phase of the competition, which has a place in the Caf Champions League as a reward for the ultimate winners.