Fernando Santos questioned the referee's performance after Portugal suffered the first defeat of their Nations League campaign to Switzerland.
Haris Seferovic opened the scoring after just 55 seconds in Geneva, the fastest goal in Nations League history and earliest Switzerland have scored since 1988.
Referee Fran Jovic awarded a penalty to Switzerland 13 minutes later for a handball against Nuno Mendes, but the VAR overruled the decision.
A clear foul on Andre Silva by Nico Elvedi on the halfway line was the reason, with the Portugal striker requiring brief medical treatment for the ankle injury suffered in the tackle.
Portugal were incensed at the original decision, surrounding Jovic at half-time, and tempers continued to boil over in the second half, with Bruno Fernandes confronting the Swiss bench at one point.
While Santos refused to directly criticise the referee's performance, he admitted his frustrations with Switzerland seemingly slowing down the game en route to a 1-0 victory.
"I'm not going to criticise, but when a penalty is awarded that doesn't happen just like that, when there's a clear foul in midfield... Then just look at the number of fouls and time lost," he told reporters.
"The fourth official knows very well what happened in the game."
Santos was satisfied with the second-half improvement, even if Swiss goalkeeper Jonas Omlin's heroics left Portugal a point behind group leaders Spain, who defeated Czech Republic on Sunday.
"At half-time, I was just saying that we have to have the ball and play differently and push them back," he added.
"We started very well, in the first few minutes we wanted to put the ball very quickly on [Goncalo] Guedes. We knew opportunities would arise and many have arisen."
Portugal are not in action again until visiting Czech Republic in the Nations League on September 24.
'One game at a time', says calm Slot after Leverkusen thrashing
Arne Slot insisted he will continue to look at "one game at a time" after leading Liverpool to a 4-1 victory over Bayer Leverkusen in the Champions League on Tuesday.
Luis Diaz's second-half hat-trick along with Cody Gakpo's 63rd-minute strike spoiled Xabi Alonso's Anfield return, moving the Reds top of the 36-team standings.
Liverpool have now won all four of their Champions League games under Slot. It’s only the second time that they have won all four opening games in a single season.
The Reds are now top of both the Premier League and Champions League, though Slot was keen to focus on the next task, which comes in the shape of Aston Villa on Saturday.
"I don't know if it was that much to do with intensity, but we took more risk," Slot said.
"They overloaded the midfield a lot, and we adjusted at half-time and took the risk to play one v one all over. We had better chances in the first half and they weren't a goal threat.
"As much as this time, how good they are in Europe, sometimes a strong target man is better than someone a bit faster.
"Curtis Jones did an incredible pass, and then you have someone with the pace of Lucho to finish it off. The pass was as good as the goal, in my opinion.
"You don't look ahead as a manager in the next three months. You're always one game at a time. We've got Aston Villa on Saturday, another tough game."
Diaz's treble saw him become only the second Colombian player to score a hat-trick in the Champions League, after Faustino Asprilla for Newcastle against Barcelona in 1997.
And he insisted that things have started brightly for Slot at Anfield, but said his team-mates must continue to perform to have something to show for it at the end of the season.
"The most important thing is the three points in this edition of the Champions League so we can keep progressing in the competition," Diaz said.
"Things have gone so well with the new manager, it wasn't easy for him to come in and fill Jurgen Klopp's shoes.
"Hopefully, we'll have something to show for it at the end of the season.
"We have top-quality players all over the pitch and I really enjoyed playing in that position today. I'm just happy to be on the pitch.
"I need to go and find that ball now because I need to keep it somewhere special at home."
For Alonso and Leverkusen, meanwhile, it marked a first Champions League defeat since 2022, while also conceding four or more goals in an away match in the competition since 2013 against Manchester United.
"It's painful the result more than the performance, probably," Alonso told Amazon Prime.
"But this is the Champions League, this is the highest level, and today it wasn't enough for us."
"It's too early to tell, but I can see that Liverpool have a very good balance, a very complete team.
"They work with 11 players, and they have the power to hold a clean sheet, which is important in the Champions League.
"In the Premier League, let's see. It's early to tell but it's looking good."
Alonso, who won the Champions League with Liverpool in 2005, was serenaded by the home supporters at Anfield during the contest.
"I tried to separate the game and the pain from the result from the nice feelings to come back. I'm really happy and thankful for that reception," he added.
Bologna 0-1 Monaco: Kehrer maintains visitors' impressive Champions League start
Monaco defender Thilo Kehrer scored a late goal to earn a 1-0 Champions League victory for his side at Bologna on Tuesday.
Monaco captain Kehrer, left unmarked in front of goal four minutes from time, stretched out a leg to poke the ball home from a flicked-on corner to snatch the points.
The visitors maintained their unbeaten start to this season’s Champions League while also dealing Bologna their first-ever home defeat in European competition.
Both sides saw goals chalked off in the first half, Monaco's Wilfried Singo being penalised for a foul on Lukasz Skorupski before Santiago Castro saw a curling strike disallowed for a foul in the build-up.
The two Polish goakeepers, Monaco's Radoslaw Majecki and Bologna's Skorupski, both made several fine saves to keep the game goalless until Kehrer got the all-important touch on an inswinging corner late on.
The win puts Monaco in third place with 10 points, while Bologna are down in 30th spot with one point after four games.
Data Debrief: Long-awaited shutout for Monaco
Monaco have now won consecutive games in the Champions League for the first time since a run of three in 2017, also ending a 23-game run without a clean sheet in the competition.
Bologna, meanwhile, are the only side in this season's Champions League to play four matches and fail to score, despite registering 48 shots in total and an xG tally of 3.19.
Sheffield United go second after late turnaround, Plymouth continue good home form
Sheffield United staged a late turnaround to win 2-1 away to Bristol City and go second in the Championship, one point behind leaders Sunderland who play on Wednesday.
The game started slowly, with the hosts not opening the scoring until a 75th-minute Anis Mehmeti penalty after a foul on Sinclair Armstrong by goalkeeper Michael Cooper.
The Blades showed great character to haul themselves back into the game, with 18-year-old Ryan One scoring the equaliser in the 86th minute.
But things went up a notch in stoppage time when Robert Dickie was given a straight red card for a cynical foul on Callum O'Hare 35 yards out.
The drama wasn't finished yet and with seconds to go, Harrison Burrows smashed home a left-foot rocket to win the game for the Blades.
At the bottom of the table, Plymouth opened a four-point gap between themselves and the relegation zone with a 1-0 victory over bottom-of-the-table Portsmouth.
The victory means that Wayne Rooney's side have dropped just two points in their last five games at Home Park, having lost six on the bounce in all competitions away.
It is now four without a victory for Portsmouth, who have earned just nine points in their opening 14 matches back in the Championship.
Elsewhere, Middlesbrough responded to their 3-0 defeat at home to Coventry City last weekend by beating second-bottom Queens Park Rangers 4-1 on the road.
That was a first victory in three for Michael Carrick's side, who are one place below the play-off positions and trail only by goal difference.
QPR are four points behind fourth-bottom Preston North End, having failed to win any of their last 10 league games.
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