Fans spoke out after the two exchanged niceties on the Tuesday episode. Thomas was there to promote some projects, including her upcoming film Magical Christmas Village.
"Look how beautiful you are. You lost a lot of weight," Thomas gushed during the segment, leading Shepherd to share that she lost around 35 pounds.
The comment that ruffled feathers was made moments afterwards, when Thomas recalled a time they had reversed roles. "I interviewed you for my AOL show," the That Girl actress remembered, adding, "and you used to be a big woman!"
Shepherd didn't seem to be bothered by the remark, erupting into laughter before sitting closer to Thomas.
Thomas was giggling herself, continuing the quip by putting her hand around her body and blowing her face out to imitate the television personality's former physique.
"You've lost a lot of weight, but you've still got the boobies! That's good," Thomas added.
Despite the awkward exchange being short-lived, people on set were not pleased because they felt the comment was out of line.
"Sherri was a good sport, but people [at the show] are very protective of her," sources told Page Six, revealing they didn't take kindly to the joke made at Shepherd's expense.
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"People were not happy that she fat shamed her on national TV," added the source, claiming staffers were "very" vocal about how they felt. "It was like a slap in the face."
The source noted, "She works really hard at creating a very positive environment. Morale [at work] is everything to her, so people sort of went into mama bear mode."
Shepherd, for her part, brushed off the ordeal. "You never know what's gonna happen on #Sherri," she replied to one fan via Twitter with a laughing emoji.
Another viewer sounded off that Thomas "just acted like those elders in the church," adding that "you roll with it 'cause she's an elder!"
All in all, "Sherri laughed off the comment," Shepherd's rep said in a statement.
Thomas also took to Twitter with a photo of the duo while congratulating Shepherd on her success. "I had so much fun with my old friend @sherrieshepherd. So happy she has her own show, @sherrishowtv," her caption read. "She deserves it!!"