Wolves and Rui Patricio have been reported to Fifa by Sporting Lisbon over the transfer of the goalkeeper from the Portuguese club.
The 30-year-old, Portugal's number one at the World Cup, was one of nine Sporting players to terminate their contracts after an attack by fans.
He joined newly promoted Wolves in June, but Sporting are reported to want £48m compensation for the player.
Fifa told BBC Sport it had received a complaint against Wolves and Patricio.
A group of 50 fans reportedly attacked Sporting players and staff in May, after the club missed out on a Champions League place on the final day of the season.
In April, former president Bruno de Carvalho claimed to have suspended 19 first-team players after a Europa League defeat by Atletico Madrid, although he deleted the post on social media and most of the players featured in their next game.
De Carvalho has since quit the club after fans voted for him to resign, with Sousa Cintra put in temporary charge until elections are held in September.
Sinisa Mihajlovic, De Carvalho's managerial appointment, was sacked after nine days and replaced by Jose Peseiro, who has returned for his second spell at the club.
Midfielder Bruno Fernandes, one of the nine to quit, re-joined the club on Tuesday, signing a new five-year deal with a 100m euro release clause.
"It doesn't matter who is to blame, now it is over," said Fernandes. "Sporting are opening a new page and I believe it will be very good."
Nani returns to Sporting
Nani, 31, has returned for his third spell at the club, joining on a two-year deal on Wednesday.
The former Manchester United winger spent last season on loan at Lazio from Valencia.
He started his career at Sporting before joining United in 2007 and also had a season-long loan spell back at Sporting in 2014.
"It's important for me to go back home to feel cherished again," he said. "I'm in the club's body and soul."