"So happy for your union. Love is amazing. It's wonderful," the 'Happy' singer said to Meghan and Harry.
"Don't ever take that for granted but what it means in today's climate, I just wanted to tell you it's so significant for so many of us. Seriously. We cheer you guys on."
But it was Meghan's response that raised eyebrows.
"Thank you, they don't make it easy," the ex-actress replied.
The Duchess's shocking comment follow weeks of tension for Meghan.
The new-mum was mummy-shamed for holding baby Archie awkwardly at a polo match last week.
She also caused controversy after she instructed her royal security personnel to inform spectators at Wimbledon not to take photos of her.
However, she was all smiles at the Wimbledon women's final, which she attended with her sister-in-law, Kate Middleton.