The 22-year-old was withdrawn in the 68th minute against Arsenal in last week's 1-1 draw at Stamford Bridge, with Mykhailo Mudryk replacing him.
He was then caught on camera walking immediately down the tunnel instead of taking his seat alongside his teammates in the Blues dugout.
Boss Enzo Maresca discussed the incident post-match, where he defended Madueke, claiming that no player is happy when they are taken off.
Madueke's reaction led to Rio Ferdinand blasting the England international as 'disrespectful', while insisting he should face punishment from the west London giants.
Speaking on his YouTube channel, the Manchester United legend said: "You think (Danny) Welbeck or Tom Cleverly or Nani are going to storm off the pitch and throw their dummy out?
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"It's disrespectful to your teammates as well. It's a young team. Who are the experienced players who are going to go in there and say, 'Woah, we don't accept that here.'
"I think the manager protecting him is mad. And that's why I couldn't be in there [as a manager].
"Because I couldn't come out and play the game where you say, 'Yeah he was in the wrong but [he's a good kid]'. Fined, that's a two-week fine."
Even Chelsea cult hero and former coach Jody Morris lamented Madueke when speaking to talkSPORT, insisting he would be 'fuming' if he was the player's teammate.
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But Madueke has now set the record straight over his sharp exit as he stated outrage aimed at him has been a massive misunderstanding.
He said: "'I literally went down the tunnel to go to the toilet and I came back 30 seconds later.
"If you watch a lot of games when I come off, I always going straight down the tunnel to go to the toilet.
"It is nothing major at all."
Madueke has been a key player for Chelsea this term - starting the last ten matches in the Premier League.
He is just one goal shy of equalling his haul of five top-flight goals from last season.
Though three of his four strikes this term came in the 6-2 win away at Wolves on August 25.
Still, his form has seen him included in the last three England squads for their Nations League qualifying campaign.
He has featured in the last four matches under interim boss Noni Madueke.
Following Arsenal star Bukayo Saka's withdrawal due to injury, Madueke was handed his first international start in the 3-0 midweek win over Greece at the Olympic Stadium in Athens.
It was Madueke who supplied the assist for Ollie Wakins' opener to show he is up for the task of rivalling Saka for a staring spot.
Commenting on the competition for places at England, Madueke said: "I don't look at Bukayo like competition.
"I look at Bukayo as a team-mate who plays for England. I know his quality and he is a player that I look at to try and implement parts of his game into mine.
"I don't look at him like, 'I am coming for you.'
"The manager will make his decision and I am happy to be part of this team, and to start to make a difference for England this early on in my career is great.
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"I feel like I did my job. I created the first goal and I was a threat pretty much until I came off. That is what I try to bring every time I step on the pitch."
Madueke will be hoping to keep his place in England's final National League clash with Ireland at Wembley on Sunday.