Mainoo's half-brother Jordan Mainoo-Hames was spotted wearing the eye-catching t-shirt during United's 4-4 draw with Bournemouth at Old Trafford, where the midfielder came on for the last half-hour on Monday.
Mainoo has yet to start a Premier League game this season and has been restricted to 11 appearances off the bench but Amorim made clear that the t-shirt would have zero impact on team selection at Aston Villa on Sunday.
"No, it wasn't Kobbie who was wearing the t-shirt. He's not going to start because of the t-shirt, but he's not going to the bench because of the t-shirt. He is going to play if we feel he is the right guy to play," Amorim told reporters.
"So that is not an issue. I've been here for a year, it's not new. We have to deal with it but I am not going to do something to Kobbie because someone in his family is doing something.
"It's going to be the same. If he's the right guy to play, he is going to play."
Fernandes 'hurt' by United
Amorim is also managing discontent from captain Bruno Fernandes after the Portugal midfielder told Canal 11 that he was hurt that the club wanted him to leave when Saudi Pro League side Al-Hilal showed interest.
Fernandes said he could have left in the close-season transfer window but stayed not only for his family but because he 'genuinely' loved the club.
"He said what he is feeling. We already know the noise but he talked with the board and I think everything is clear," Amorim said.
"We just spoke about his feelings and he needs to answer to that, not me. He gives everything and puts everything on the line. We need to step up and also have that feeling.
"He is a big example in the group. He spoke his feelings and when I watch him training and playing, he is a special character."
Surprise title contenders Villa
United face a Villa side who have emerged as surprise title contenders with Unai Emery's side sitting third in the standings, three points off leaders Arsenal and a point behind Manchester City.
Villa have won their last nine home games in the Premier League to turn Villa Park into a fortress and Amorim suggested they could indeed compete for the title.
"Everything can happen. They have a manager with a lot of experience. When you watch Villa play you can sense it's a very mature team," Amorim said.
"Unai Emery doesn't panic when he's losing, he doesn't feel overwhelmed when he's winning. He controls his emotion all the time.
"They are a very strong team. Can they fight until the end, I don't know, but they are capable of that."