The Three Lions were beaten 2-1 by the defending champions, with Harry Kane converting one penalty to level it up early in the second-half but he missed a second spot-kick with five minutes remaining.
That left Olivier Giroud’s header as the winner, and England heading home as their campaign in Qatar came to a painful end at the last-eight stage.
The second of those penalties was only given after a VAR review, while England felt they should have had an earlier spot-kick when Dayot Upamecano appeared to bring down Kane in the first-half.
Replays also suggested that Bukayo Saka was fouled in the build-up to Aurelien Tchouameni’s opener, and the Arsenal man had a number of appeals waved away during the match when he was seemingly fouled.
Speaking after the game, Maguire revealed his frustration at the officiating from Brazilian Wilton Sampaio.
“I can’t really explain his performance,” Maguire told ITV.
“The amount of decisions they got wrong was actually incredible. Really poor.”
Team-mate Jude Bellingham was also disappointed at a number of decisions made, in particular the call not to award England a penalty from Upamecano’s trip, which took place right on the edge of the box.
“Not great if I’m being honest,” Bellingham said.
“Anyone can have a bad game, players and referees. He wasn’t where he should have been today in terms of the level for a game like this.
“But there’s more factors as to why we lost, this is definitely not me putting it all on him.”
He added: “There were a few around the box, we know how deadly we are from set-pieces.
“Any one of those can make the difference. There was one from Upamecano for a penalty in the first-half.”
Referees have been in the spotlight throughout the quarter-final stage at the World Cup, most noticeably in Argentina’s win over the Netherlands. Antonio Lahoz gave out 18 yellow cards in that match, drawing criticism in particular from Emi Martinez and Lionel Messi.
Gary Neville echoed the views of the England players, giving a slightly more undiplomatic view on the officiating.
“The referee had a nightmare game, an absolute joke of a referee,” Neville said.
“I’m not saying that was all down to England’s defeat because that’s making excuses. He was just a bad referee, rank bad.”