The airline was criticised by Dame Gillian Morgan, who told Metro she had seen all the boys on her TUI Airways flight with pilot stickers and all the girls with cabin crew stickers.
"The stickers were gender neutral but it’s the way that they were handed out that makes it complicated," she said.
Metro also quoted social media posts from two other people who had flown separately with TUI claiming cabin crew stickers were given to girls and pilot stickers to boys.
TUI said in a statement: "We’re sorry to hear a small number of customers have been upset by this. We think it has just been a simple mix-up since our future pilot and cabin crew stickers are designed for use for any child regardless of gender.
"The stickers are part of our activity packs which are intended to be used by crew to interact, engage with and create special moments for our customers on their holiday. The feedback we’ve had so far this summer has been overwhelmingly positive. Children fall in love with flying when they go on their holidays with us and we want to encourage their dreams of becoming future pilots and crew members."