The French centre-back was sent off in the 19th minute of the 3-0 defeat at the Etihad Stadium on Monday night after sliding in with his studs showing.
His challenge won the ball but also caught City's former Monaco man.
"It was quite a hard tackle but I am fine," said the Portuguese midfielder, 24.
"Yes he did [apologise] at the end of the game. These things happen.
"You don't do it on purpose, I think, and he said that. Everything's fine. It's football."
Wolves boss Nuno Espirito Santo said referee Craig Pawson made the correct decision in dismissing the 27-year-old.
"It's very close to me and I think it's a red card," he said. "It's clear, you saw it. It's a red card."
However, former Premier League referee Mark Clattenburg told The Mail he thought the decision was harsh.
“Boly was unfortunate to be sent off for his challenge on Bernardo," he said.
“You must first consider that the Wolves defender won the ball before catching the Manchester City midfielder. That does not mean it is not a red card, of course.
“But Boly’s foot was low and he caught Silva on the ankle, not on the shin or higher."
Gabriel Jesus scored twice to help City to a win that leaves Pep Guardiola's side four points behind leaders Liverpool.
City travel to the Premier League's bottom club Huddersfield on Sunday.