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The Brazil striker, who scored Wolves' equaliser at Molineux, "allegedly acted in an improper manner" during a confrontation between the two sides at the final whistle.
Post-match footage appeared to show Cunha elbowing a member of Ipswich's security team in the back of the head before snatching the glasses off the man's face.
The 25-year-old has until 19 December to respond to the charge.
In the wake of the defeat - which was Wolves' 11th in the Premier League this season - the club sacked manager Gary O'Neil and his backroom staff.
Cunha has scored eight goals in 16 top-flight appearances this season but could face a ban for his role in the incident.
Jack Taylor's last-gasp header gave Ipswich victory and at full-time, Cunha's team-mate Rayan Ait-Nouri was sent off in the tunnel for a second yellow card.
Wolves are 19th in the Premier League, five points behind 17th-placed Leicester City who they play on Sunday at 14:00 GMT.
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