The retired lighting director, 73, blindsided Meghan Markle and Prince Harry when he gave his first TV interview on Monday.
During the surprise appearance, Mr Markle spoke about private conversations he had with Meghan and Harry, speculated the couple will have kids “soon” and revealed the Prince’s feelings on United States President Donald Trump.
Sources told ET that his appearance had driven a wedge between the royal newlyweds and Mr Markle.
“It came as a surprise. They were not given advanced warning,” the source claimed. “They understand he has been harassed by the paparazzi 24/7 but it’s hard for them to accept his apology when he’s again taking cash.”
Meghan and Harry have “tried to offer him support and guidance” when it comes to the media, but it was being made difficult by Mr Markle’s actions, the source alleged.
“The relationship is fractured and it will be interesting to see where they go from here,” they added.
Good Morning Britain host Piers Morgan has confirmed Thomas was paid “a few thousand pounds” for the interview, but it hadn’t been about the money.
“The real motivation was setting the record straight, having his say,” Morgan told ET.
Mr Markle’s TV appearance comes after he dramatically pulled out of attending the royal wedding last month.
He began suffering heart issues and had to have emergency surgery after it was revealed he had been staging paparazzi photos.
After Mr Markle was unable to attend Prince Charles stepped in to walk Meghan down the aisle instead.