Earlier this month on Twitter, Allen made an apparent dig at Cotton's Radio 1 music show, which Cotton replied to almost immediately.
Allen wrote: "Fearne cotton is such a trendsetter. Listening to radio 1 in amazement (sic)."
Cotton responded: "Not sure if lilyroseallen is being sarcastic or just nice? Thanks either way lilly (sic)."
A source later told Heat: "Lily can't stand Fearne. She thinks she represents everything shallow and pointless about TV and, albeit peripherally, the music industry.
"She's really fed up at the moment and has been stuck indoors for ages. She doesn't know what she wants to do with her career and is taking it out on anyone she can."
One of Cotton's friends reportedly told the publication: "[Fearne] hasn't given it any more thought - she's so busy right now."
In March, Allen suggested that the then-planned axe of BBC 6 Music would result in the end of "acts like Seasick Steve and presenters like Lauren Laverne", leaving only "the Pussycat Dolls and Fearne Cotton on Radio 1".
> Lily Allen announces pregnancy