Apprentice Ben Thompson has won a staying race at Flemington, but not on the horse he thought he might have steered to victory.

Thompson was booked to ride in-form stayer De Little Engine in Saturday's Young Members' Ball Handicap (2500m) but the Danny O'Brien-trained gelding was scratched on Friday.

It left Thompson without a mount but he then picked up the ride on Falago after apprentice Mitch Aitken was stood down by stewards on Friday.

Chief steward Terry Bailey said Aitken has been stood down due to an irregularity in a urine sample taken from Seymour trackwork on May 24.

The Darren Weir-trained Falago was sent out a $21 chance and caused an upset as he finished over the top of odds-on favourite Goathland ($1.65) to win by a length with a short half-head to Try Four third.

"The horse on the day was rock hard fit and he got the job done," Thompson said.

"It was a real dampener on my day (when De Little Engine was scratched). I thought I had a nice book and the horse I thought was the best of them was scratched.

"But it was a fortunate pick-up ride on Falago."

The Darren Weir-trained Falago had been out of the placings in five starts this preparation over shorter distances and managing owner Darren Dance said retirement had even been considered before it was decided to step him back up to 2500m.

"This is his distance," Dance said.

Falago was placed in three 2500m races, including two at Flemington, during the winter months last year.