Atkinson then changed his mind thanks to VAR, deciding the challenge was only worthy of a yellow card, but during the process Lindelof appeared to get himself into a war of words with the Wolves bench.
Lindelof played for Benfica from 2012-2017 and appears to have become fairly proficient in Portuguese, with lip-readers thinking they spotted what he said in the language.
It remains to be seen if the player will face any disciplinary action for his outburst, and it is not known what caused him to react so angrily.
Lindelof has been virtually an ever-present in the United side this season, making 33 appearances in total with one goal to his name.
After the match caretaker manager Ole Gunnar Solskjaer expressed his frustration at going out of the FA Cup, a competition which he won twice as a player at Old Trafford.
He said: "This was the poorest we've played. We started too slowly and played into their hands. Our possession wasn't bright enough and quick enough, so it's disappointing.
"This was a big step backwards, mainly because of the quality of the possession and the passing."
Manchester United are yet to comment on the alleged incident.