Thomas Tuchel shared that he regretted not speaking with Manchester City stars in his England squad before kick-off against the Czech Republic.
City were found guilty just hours before for serious breaches of Premier League financial rules between 2009-10 and 2017-18.
The Premier League released a statement confirming the news, with sanctions to be set out in a further hearing with the independent commission.
Despite the news, Elliot Anderson, Marc Guehi and Nico O'Reilly all travelled with the squad and started in Prague.
"I have a bad conscience now," Tuchel told the BBC when asked if he had spoken to the trio.
The German continued: "I did not actually because I am just focused on everything we have to deal with here and to prepare the team."
The chief executive of the Premier League, Richard Masters, said the findings "vindicated" the league's decision to pursue the probe against City.
He said: "The core decision establishes the facts of what happened at Manchester City during this period.

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"It details how the club systematically broke Premier League rules for nearly a decade. It also vindicates the Premier League's decision to pursue this case against Manchester City.
"While the process to date has been both long and difficult, the league has remained determined that the facts be established independently.
"It is a key responsibility of the Premier League to ensure that the rules, approved by the clubs themselves, are upheld to protect the integrity of the competition.
"It is paramount that the league remains competitive and fair for all clubs and for the fans. We take that role extremely seriously."

The City trio helped secure a 2-0 win for the Three Lions against the Czech Republic's 10-men.
Goals from Anthony Gordon and England's skipper Harry Kane mean the Three Lions move up to second in their group.
Tuchel praised Jude Bellingham's role, saying the Real Madrid star could be captain one day.
He said: "If you are the captain at the end of these matches you can for sure be the permanent captain.

"I think he loves to be with us at the moment. That's what I feel. We had this small talk today about his role, and we both had our hearts or stomachs say, 'let's go again, let's start (the match) again.'
"Then both our heads said, 'Maybe 30 minutes is enough for today,' because he hasn't played this quick turnaround through this season.
"He has done it before but not in the season so we didn't want to be the first ones to try that.
"But even in this little encounter, you can see he is confident and happy to even help from the bench so yeah, it is a reward. It is good. He had a little niggle at the end of the match, hopefully it is nothing serious and he is available for Croatia."
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