Wolves manager Mick McCarthy made 10 changes to the team who defeated Tottenham Hotspur three days earlier and, after a 3-0 loss at Old Trafford, recalled nine of them for the next game against Burnley, which they won 2-0.
Wolves said they had been surprised to be charged but accepted the decision.
"We are obviously disappointed but we respect the ruling, especially as they have now used our case as a clear warning to all other clubs, some of whom have made similar changes to their teams in the past, that this is not acceptable in the future," Chief Executive Jez Moxey said in a statement on the club's website.
"This ruling may now lead to a wider discussion regarding the issue of squad rotation and the Premier League's rules."
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