Brendan, who was partnered with celeb dancer Charlotte Hawkins, had rowed with Shirley over her comments and marks in this year's live shows.
Despite having been voted off the show, The Sun reported that Brendan was still annoyed at Shirley over her feedback.
And, apparently, getting the new judge job over him.
"Brendan is clearly very bitter about missing out on the role and hasn’t held back on taking out his anger on Shirley," a source accused. “He goes out of his way to ignore her backstage during show breaks and makes her feel very uncomfortable."
The insider alleged to The Sun newspaper: “Brendan notoriously falls out with fellow dancers, but this row is on a whole other level. Everyone thinks it’s very childish.”
But Brendan played down the claims in an interview on ITV's Lorraine.
He explained: "[A newspaper] reported that I was hurling abuse over the balcony and I wasn't. If someone is undermarked we all go 'undermarked! Undermarked!'"
Brendan went on to say he didn't regret speaking up, explaining: "I tend to be more argumentative than the rest of the pros. The rest will be [in the change rooms yelling] left, right and centre, but I don't control myself for the change room I have to do it live on air.
"I'm a nice person - my wife will tell you. I don't hold back and morally I'm big on doing the right thing at the right time and I had to stick up for Charlotte from Shirley."
Meanwhile, Shirley has hit back at her critics.
After a controversial dance off decision last week, she told the Daily Mail newspaper: "I judge with no fear or favour, but it has been a very tough week and I really don’t like to see somebody go home.
“But I entirely stand by my decision and that will never change. Don’t anyone tell me how to do my job – I’ve been doing this since I was 16.”
Strictly Come Dancing continues this Saturday and Sunday night on BBC One.
The series will be coming live from Blackpool's iconic Tower Ballroom.