The edited episode was from 1994 and entitled 'Homer Loves Flanders', featuring Homer Simpson and his religious neighbour Ned Flanders striking up an unlikely friendship.
As they drive away from an American Football game together, Homer decides to make their relationship public.
He says: "I want everyone to know that this is Ned Flanders... my friend!"
Standing in the car park, Homer's friends Lenny and Carl overhear this, and Lenny asks: "What'd he say?"
Carl's original reply was: "I dunno. Somethin' about being gay."
However, when the episode was aired on a Sunday at 12.55pm, Channel 4 instead cut straight to an ad break before Carl speaks.
But speaking to The Independent, Channel 4 admitted to making a mistake by judging that the word 'gay', in its homosexual context, was not suitable for a Sunday lunchtime.
The broadcaster confirmed that the "error" occurred due to overzealous programme compliance.
"We always carefully consider the context in which language is used in our programming," said the broadcaster.
"However in this instance the episode was edited in error as neither the word nor the context was unsuitable."
It only becomes offensive when used in a context that "results in a negative portrayal of homosexual men and women".
In 2009, former BBC Radio 1 breakfast presenter Chris Moyles came under fire from Ofcom for comments he made about Will Young's sexuality on air.
Eight people complained to Ofcom that Moyles's alternate versions of Young's songs 'Evergreen' and 'Leave Right Now' featured remarks that "were offensive and derogatory towards the gay community".
Mimicking 'Leave Right Now' to mark the singer's birthday, Moyles had sung: "Oooh Will Young here, mmmmh. I'm here, it's Will's birthday and as the years go by I get more very gay. When you saw me years ago you didn't know, but now I'm the gayest fella you probably know. Mmm I like to wear a silly hat, I get camper by the hour, oh would you look at the muck in here. I'm Will Young and I'm gay."
The BBC attempted to argue that Moyles's audience "would have been clear that such remarks were not intended to be hostile or derogatory", but Ofcom said that such mentions were not justified by the context.