In a frustrating night for City in the Russian capital they surrendered a two-goal lead to draw 2-2.
Captain Vincent Kompany claims it is "unacceptable" Manchester City had no fans at their Champions League tie at CSKA Moscow while the home side apparently did.
CSKA appeared to have around 200-300 fans backing them at a game that was officially played behind closed doors at the Khimki Arena.
European governing body UEFA ordered the stadium to be closed as punishment for persistent offences by CSKA fans, who have been found guilty of racist behaviour three times in the past year.
Despite that, 650 people were still permitted to attend and the CSKA supporters who vocally backed their team were thought to have come from within an allocation of 300 tickets set aside for sponsors.
You say 'no fans' then all of a sudden you turn up and basically the only team that hasn't got fans is Man City. So who's getting punished? Who is being done for racism? Man City or Moscow?
I don't have a problem, they'll say it's sponsors and so on and they need to give certain allocations, but why are we getting punished?
Fernandinho claims playing in an empty stadium in Moscow is of no benefit to Manchester City's Champions League quest.
No fans will be present as the Khimki Arena on Tuesday as City take on CSKA Moscow in a crucial Champions League Group E game.
CSKA have been ordered to play their next three European home matches behind closed doors as punishment for the racist behaviour of their fans.
The Russian side will therefore not have a partisan home crowd to motivate them but Fernandinho disagrees with suggestions that is to City's advantage.
I don't think it will be an advantage for us. It is always good when you play away because the fans support their team and it gives you more motivation to play well.
I don't think this is good for either team or for football.
There are some anecdotal reports of City fans planning to watch from a neighbouring high-rise building, but the English champions will have to go it alone.
Gareth Bale has been left out of Real Madrid's squad for Wednesday's Champions League clash against Liverpool as the Wales international battles a muscle injury.
Bale was unlikely to feature at Anfield after Madrid announced on Monday that the forward was suffering from a gluteal injury, and on Tuesday the world's most expensive player was a confirmed absentee from Carlo Ancelotti's 20-man squad for the trip to Anfield.
The 25-year-old was an unused substitute in Saturday's Primera Division win over Levante on his return from international duty, having played the full 90 minutes in both of Wales' Euro 2016 qualifiers against Bosnia-Herzegovina and Cyprus.
Madrid, the reigning European champions, will be defending their 100 per cent record in Champions League Group B at Liverpool, who have won one and lost one so far.
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Liverpool manager Brendan Rodgers insists his side cannot become too focused on stopping Cristiano Ronaldo in the Champions League this week as Real Madrid have enough quality to hurt them elsewhere.
Real's other flying forward Gareth Bale is unlikely to feature because of an injury which kept him out of the weekend's 5-0 win over Levante but Ronaldo will undoubtedly take centre stage in the Group B clash at Anfield on Wednesday.
The Portugal international arrives on the back of breaking at 71-year La Liga record by scoring 15 goals in the first eight matches of the season and while his talent cannot be under-estimated, Rodgers stressed it would be foolish to focus solely on him.
They are as strong a team now as they have been for many years. They have everything, big experience, big players, speed, technique and a great manager in (Carlo) Ancelotti, a good man who works with players and who is a good person.
Liverpool go into game on the back of a poor performance at QPR which - even though ended in victory - did little for confidence.
Captain Steven Gerrard admitted afterwards if they reproduced a similar display against Real they would have "no chance" of winning, but Rodgers believes the status of the fixture will bring out the best in his players.
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Real Madrid winger Gareth Bale is battling for fitness ahead of Wednesday's Champions League match at Liverpool after the club announced he is suffering from a buttock muscle injury.
The 25-year-old Wales star was an unused substitute in Saturday's Primera Division win over Levante on his return from international duty, while reports in Spain said he also sat out training on Monday.
That raised doubts over Bale's availability for the trip to Anfield, as well as this weekend's El Clasico with Barcelona, although Madrid have said for now they will keep an eye on the player.
Phil Jones is determined to make sure Manchester United's absence from the Champions League is just one season long.
United crashed out of Europe's premier club competition - beaten 3-1 by holders Bayern Munich, with the quarter-final tie lost 4-2 on aggregate.
As David Moyes' men sit seven points adrift of fourth place in the Barclays Premier League with five matches left, it would take a minor miracle for the team to qualify for the competition next season.
That means United will miss out on playing in the tournament for the first time in 19 years.
"It's hugely important we get back in it as soon as possible," the United defender said.
"Manchester United need to be in the Champions League.
"Nights like these do not come around too often. They are the ones you look back on and think - 'what a time that was'.
"You want to play against the best and you want to test yourself against the best.
"We believe it will be. We are confident we be right up there challenging next season.
"This wasn't the way we wanted it to end. I thought we more than held our own against them tonight.
"We didn't disgrace ourselves against a really good team but we are still disappointed."
Manchester United's Champions League dream is over after a resounding defeat away to Bayern Munich.
It was a tough night for Manchester United in Munich. They're out of the Champions League - beaten by Bayern Munich 3-1. Patrice Evra put them in the lead for just 73 seconds.
Manager David Moyes - already under pressure for disappointing results at home will have to head back to face the music.