Roberto Martinez said he did not substitute Kevin Mirallas for disobeying orders and taking a penalty from teammate Leighton Baines and then missing it in Everton's 0-0 draw against West Bromwich Albion.
Baines, who has scored 15 of 16 Premier League penalties for Everton, is their first-choice spot-kick taker, but winger Mirallas argued he should step up after Joleon Lescott handled and then struck the post.
Mirallas did not return for the second half and manager Martinez claimed the Belgian was replaced because of a minor hamstring injury and not because of his conduct.
The Everton manager said in a news conference: "When he gets in at halftime and the body temperature changes, he felt his hamstring was starting to give him a bit of a problem.
"He has been carrying a problem. That is why he didn't start against Manchester City and West Ham. He wasn't 100 percent to start the second half. He was 100 percent for the first half."
Martinez said Baines was "happy" for Mirallas to take the spot kick, although on the pitch teammates Steven Naismith and Romelu Lukaku seemed to be urging the winger to let the left-back try and beat Albion goalkeeper Ben Foster.
"Our penalty taker is Leighton Baines," Martinez said. "He is the No. 1 penalty taker but we have a few players in the squad capable of taking them. At that moment Kevin felt really confident and wanted to take it.
"Both players have enough quality, personality and character to convert. It became an issue because he couldn't find the back of the net. Leighton was quite happy to let him take it because he felt confident."
Martinez denied the incident showed a lack of team spirit in the Everton camp, arguing: "If it has been the other way around and Leighton says no, the issue would be why Kevin was not allowed to take the penalty. We are a team that is very, very together."
However, Martinez was asked who he wanted to take Everton's next penalty and replied: "Not Kevin."
Everton have now gone eight games without a win and Martinez rued the missed penalty and the result, saying: "It is a key moment in the game. The first goal was going to be important. If you play this game 10 times it would be nine wins for us and one draw for West Brom. That is the moment we are in."
Naismith defended Mirallas after his penalty miss and said his teammate's confidence was high after he scored his penalty in the FA Cup shoot-out against West Ham last week.
"We've won the penalty and the ball's fallen to Kev and Kev has felt confident, he showed in the West Ham he was very confident then and he slotted his penalty away," Naismith told Sky Sports 1. "He's in form and he's playing well and he wanted to step up and take it and unfortunately he's missed.
"We should have had enough in the 90 minutes to win rather than relying on the penalty taker."
He added: "Bainesy had a very good record and then he missed at Man United which was disappointing for him.
Martinez said midfielder Muhamed Besic was substituted with a knock to his foot.
Information from Press Association was used in this report.